Alignments for a candidate for putA in Amantichitinum ursilacus IGB-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Amantichitinum ursilacus IGB-41

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_053939191.1 WG78_RS17855 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>NCBI__GCF_001294205.1:WP_053939191.1
          Length = 1316

 Score = 1925 bits (4988), Expect = 0.0
 Identities = 1008/1344 (75%), Positives = 1120/1344 (83%), Gaps = 41/1344 (3%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGN----IPHETSAA 56
            M+TTTLGVKLDD +R+RLK  AQ ++RTPHWLIKQAIF  L+QVERG+    +P E  AA
Sbjct: 1    MSTTTLGVKLDDLTRDRLKTAAQQLERTPHWLIKQAIFNLLDQVERGHPVVALPDEADAA 60

Query: 57   GTGSEGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLE 116
             T            +    DG++QPFLEFAQ+VQPQSVLRAAITAA+RRPE+EC+P+LL+
Sbjct: 61   ATD-----------EAPKRDGSVQPFLEFAQNVQPQSVLRAAITAAWRRPETECIPLLLQ 109

Query: 117  QARLPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEAL 176
            QAR+P  QA+AA  +A TLA +LR +  G  REGLVQGLI EFSLSSQEGVALMCLAEAL
Sbjct: 110  QARMPEAQAKAATQLAHTLAGKLRAQNPGASREGLVQGLIHEFSLSSQEGVALMCLAEAL 169

Query: 177  LRIPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKAL 236
            LRIPDKATRD+LIRDKI+  NW SH+GQSPS+FVNAATWGLL TGKLV+THTE+GLS AL
Sbjct: 170  LRIPDKATRDSLIRDKIARGNWHSHIGQSPSLFVNAATWGLLLTGKLVSTHTESGLSTAL 229

Query: 237  TRIIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAM 296
            TRIIGK GEP+IRKGVDMAMRLMGEQFVTGETISEALANAR +E  GFRYSYDMLGEAAM
Sbjct: 230  TRIIGKRGEPVIRKGVDMAMRLMGEQFVTGETISEALANARNFEGHGFRYSYDMLGEAAM 289

Query: 297  TEADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGR 356
            T+ADA  Y+ASYEQAI AIGQAS GRGIYEGPGISIKLSALHPRYSRAQHERVI ELY R
Sbjct: 290  TDADAHAYMASYEQAIRAIGQASGGRGIYEGPGISIKLSALHPRYSRAQHERVISELYPR 349

Query: 357  LKSLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPF 416
            +K+LT+LARQ+DIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQ YQKRCP+
Sbjct: 350  VKALTVLARQFDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQAYQKRCPY 409

Query: 417  VIDYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARK 476
            V+DY+IDLA+RS HRLMIRLVKGAYWDSEIKRAQ+DGLEGYPVYTRKVYTDVSY+ACARK
Sbjct: 410  VLDYIIDLAKRSGHRLMIRLVKGAYWDSEIKRAQIDGLEGYPVYTRKVYTDVSYLACARK 469

Query: 477  LLSVPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536
            LL  P+ +YPQFATHNAHTLAAIYQ+AG NYYPGQYEFQCLHGMGEPLY+ VVG  A+GK
Sbjct: 470  LLGAPEAVYPQFATHNAHTLAAIYQMAGQNYYPGQYEFQCLHGMGEPLYEHVVGKAAEGK 529

Query: 537  FNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMH 596
             NRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIAD +I+L++LVADPV VVEQM 
Sbjct: 530  LNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADQSIALEDLVADPVVVVEQMA 589

Query: 597  ADEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLG 656
              EG  GLPHP I  PR LYGE+RANSAG+DL+NE RLASLS+ALL  T  A  A P   
Sbjct: 590  RQEGTQGLPHPSIPLPRALYGEARANSAGLDLANEQRLASLSAALL--TDHAWLATP--- 644

Query: 657  TEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAA 716
              AAAGE       VRNP+D RDVVG+V EA++ +V AAL  A NA PIWQATPA  RAA
Sbjct: 645  PHAAAGE----KQAVRNPADHRDVVGYVVEAALDDVAAALTRAQNAGPIWQATPAVTRAA 700

Query: 717  ALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRP 776
             LERAA+LMEA+MQ+LMG+IVREAGKT SNAIAEVREAVDFLRYYAAQVR +FS+DTHRP
Sbjct: 701  LLERAADLMEAEMQTLMGLIVREAGKTLSNAIAEVREAVDFLRYYAAQVRGSFSNDTHRP 760

Query: 777  LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAV 836
            LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVR+L EAGVP  AV
Sbjct: 761  LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILHEAGVPQDAV 820

Query: 837  QLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQN 896
            QLLPG+GETVGAALVGDARVKGVMFTGSTEVAR+LQR++AGRLDA G+P+PLIAETGGQN
Sbjct: 821  QLLPGQGETVGAALVGDARVKGVMFTGSTEVARILQRNLAGRLDAHGQPIPLIAETGGQN 880

Query: 897  AMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGN 956
            AMIVDSSALAEQVVGDV+ SAFDSAGQRCSALRVLCLQE+VADRVL MLKG + EL +GN
Sbjct: 881  AMIVDSSALAEQVVGDVLASAFDSAGQRCSALRVLCLQEDVADRVLTMLKGGLAELVVGN 940

Query: 957  PDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIEL 1016
            PDRL+TDVGPVID EA+ NI  HIDAMRA+GR+VHQ        AAC  G+FV PTLIEL
Sbjct: 941  PDRLATDVGPVIDAEAQRNINSHIDAMRARGRKVHQVQ----TGAACNQGSFVPPTLIEL 996

Query: 1017 DSIEELQREVFGPVLHVVRYPR----AGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVE 1072
            DS+ EL+RE+FGPVLHVVR+ R    AGLD L+  INGTGYGLT+GIHTRIDETI HIVE
Sbjct: 997  DSLAELEREIFGPVLHVVRWQRTADQAGLDALIDDINGTGYGLTLGIHTRIDETIAHIVE 1056

Query: 1073 RAEVGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRAS 1132
            RA+VGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLS CP D +   V  +
Sbjct: 1057 RAQVGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSSCPRDTLHAAVLLT 1116

Query: 1133 DTVGGADETGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPT 1192
               G   ET   R  L + L  L +W+ + +   P  VA CER +AA+A G +VTLPGPT
Sbjct: 1117 SGNGAPFETA-AREQLLQPLQALAQWSAQHA---PQHVALCERLSAATAVGAAVTLPGPT 1172

Query: 1193 GERNTYTLLPRAAVLCLAQ---QETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAV 1249
            GERNTYTLLPR  VLC         DL  Q+A VLA GS+AV ++ P A A+   LPKAV
Sbjct: 1173 GERNTYTLLPREHVLCALPANGSRDDLLAQIATVLAVGSKAVVLDGPYA-AVVRELPKAV 1231

Query: 1250 QSRVRL-VADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIE 1308
            Q+R+ +  A         DAVLHHGD+DQL A+   +A R GPI+SVQGLA GE   A+E
Sbjct: 1232 QARIDVQPAGSDLATLNIDAVLHHGDADQLLALTAAMAQRSGPIVSVQGLAPGEDGFALE 1291

Query: 1309 RLLIERSLSVNTAAAGGNASLMTI 1332
            RLLIERSLSVNTAAAGGNASLMTI
Sbjct: 1292 RLLIERSLSVNTAAAGGNASLMTI 1315


Lambda     K      H
   0.318    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 4307
Number of extensions: 167
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1333
Length of database: 1316
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1267
Effective search space:  1626828
Effective search space used:  1626828
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate WP_053939191.1 WG78_RS17855 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.2788895.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-241  786.2   5.5   1.1e-240  785.3   5.5    1.5  1  NCBI__GCF_001294205.1:WP_053939191.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053939191.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  785.3   5.5  1.1e-240  1.1e-240       2     498 ..     608    1103 ..     607    1105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 785.3 bits;  conditional E-value: 1.1e-240
                             TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72  
                                            lyge+r ns+G+dlane++l+sl++ ll   ++ + a p       a ge q v+npad++d+vG+v ea 
  NCBI__GCF_001294205.1:WP_053939191.1  608 LYGEARANSAGLDLANEQRLASLSAALL--TDHAWLATPPH----AAAGEKQAVRNPADHRDVVGYVVEAA 672 
                                            8************************997..5899**99965....799*********************** PP

                             TIGR01238   73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 
                                            +++v +a++ a++a ++w+at+a  raa ler+adl+e +m +l++l+vreaGktlsnaiaevreavdflr
  NCBI__GCF_001294205.1:WP_053939191.1  673 LDDVAAALTRAQNAGPIWQATPAVTRAALLERAADLMEAEMQTLMGLIVREAGKTLSNAIAEVREAVDFLR 743 
                                            *********************************************************************** PP

                             TIGR01238  144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 
                                            yya qv+ +++++++++lG+vvcispwnfplaiftGq+aaalaaGntv+akpaeqt+liaa+av +l+eaG
  NCBI__GCF_001294205.1:WP_053939191.1  744 YYAAQVRGSFSNDTHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILHEAG 814 
                                            *********************************************************************** PP

                             TIGR01238  215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 
                                            vp  ++qllpG+Ge+vGaal  d+r++Gv+ftGstevar ++++la r da+   +pliaetGGqnamivd
  NCBI__GCF_001294205.1:WP_053939191.1  815 VPQDAVQLLPGQGETVGAALVGDARVKGVMFTGSTEVARILQRNLAGRLDAHgqpIPLIAETGGQNAMIVD 885 
                                            **************************************************87777**************** PP

                             TIGR01238  283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 
                                            s+alaeqvv dvlasafdsaGqrcsalrvlc+qedvadrvlt++kG + el+vg+p rl tdvGpvidaea
  NCBI__GCF_001294205.1:WP_053939191.1  886 SSALAEQVVGDVLASAFDSAGQRCSALRVLCLQEDVADRVLTMLKGGLAELVVGNPDRLATDVGPVIDAEA 956 
                                            *********************************************************************** PP

                             TIGR01238  354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykade....l 420 
                                            ++n+ +hi++m+a+++kv+qv++ +  ++++g+fv+ptl+eld+l+el++e+fGpvlhvvr+++      l
  NCBI__GCF_001294205.1:WP_053939191.1  957 QRNINSHIDAMRARGRKVHQVQTGA--ACNQGSFVPPTLIELDSLAELEREIFGPVLHVVRWQRTAdqagL 1025
                                            ***********************99..9**********************************975333449 PP

                             TIGR01238  421 dkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGply 491 
                                            d ++d in +GygltlG+h+ri+et+++i +ra+vGn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGply
  NCBI__GCF_001294205.1:WP_053939191.1 1026 DALIDDINGTGYGLTLGIHTRIDETIAHIVERAQVGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLY 1096
                                            *********************************************************************** PP

                             TIGR01238  492 lyrltrv 498 
                                            l+rl+++
  NCBI__GCF_001294205.1:WP_053939191.1 1097 LHRLLSS 1103
                                            ****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1316 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 42.82
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources