GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pantoea rwandensis LMG 26275

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_084935517.1 HA51_RS15475 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::P09546
         (1320 letters)



>NCBI__GCF_002095475.1:WP_084935517.1
          Length = 1314

 Score = 2135 bits (5533), Expect = 0.0
 Identities = 1077/1320 (81%), Positives = 1184/1320 (89%), Gaps = 6/1320 (0%)

Query: 1    MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPELPALLSGA 60
            MGTTTMGVKLD+ATR+RIK AA +IDRTPHWLIKQAIF+YL QLE  + LPE+   L+ A
Sbjct: 1    MGTTTMGVKLDEATRDRIKLAAGKIDRTPHWLIKQAIFNYLSQLEAGEGLPEISVQLADA 60

Query: 61   ANESDEAPTPAEEPHQPFLDFAEQILPQSVSRAAITAAYRRPETEAVSMLLEQARLPQPV 120
            A+E + AP   +E  QPFLDFAE ILPQSV+R+AITAA+RRPET+AV MLLEQARLP P+
Sbjct: 61   ASE-EGAP---DESFQPFLDFAEHILPQSVTRSAITAAWRRPETDAVPMLLEQARLPAPL 116

Query: 121  AEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180
            AE+ H+LAY LADKLR+QK A+GRAGMVQ LLQEFSLSSQEGVALMCLAEALLRIPDK T
Sbjct: 117  AEKTHQLAYSLADKLRHQKGATGRAGMVQSLLQEFSLSSQEGVALMCLAEALLRIPDKPT 176

Query: 181  RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSG 240
            RDALIRDKISNGNWQSH+GRSPS+FVNAATWGLLFTG+LVSTHNEA+LSRSLNRIIGKSG
Sbjct: 177  RDALIRDKISNGNWQSHLGRSPSMFVNAATWGLLFTGRLVSTHNEANLSRSLNRIIGKSG 236

Query: 241  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAY 300
            EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTA+DA+AY
Sbjct: 237  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTASDAKAY 296

Query: 301  MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLA 360
            ++SYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQY+RVMEELYP LKSLTLLA
Sbjct: 297  LLSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPILKSLTLLA 356

Query: 361  RQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDL 420
            R YDIGINIDAEE+DRLE+SLDLLEKLCFEPEL GWNGIGFVIQAY KRCP VID L+DL
Sbjct: 357  RSYDIGINIDAEEADRLELSLDLLEKLCFEPELEGWNGIGFVIQAYMKRCPFVIDSLVDL 416

Query: 421  ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480
            A RSRRRLMIRLVKGAYWDSEIKRAQ++GLEGYPVYTRKVYTD+SYLACA+KLLAVPNLI
Sbjct: 417  AQRSRRRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDISYLACARKLLAVPNLI 476

Query: 481  YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIY 540
            YPQFATHNAHTLAAIYQLAG NYYPGQYEFQCLHGMGEPLYEQV GKVADGKLNRPCRIY
Sbjct: 477  YPQFATHNAHTLAAIYQLAGNNYYPGQYEFQCLHGMGEPLYEQVVGKVADGKLNRPCRIY 536

Query: 541  APVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGL 600
            APVGTHETLLAYLVRRLLENGANTSFVNRIAD +LPLDELVADPVTAVEK+   EG  GL
Sbjct: 537  APVGTHETLLAYLVRRLLENGANTSFVNRIADNTLPLDELVADPVTAVEKMGASEGAVGL 596

Query: 601  PHPKIPLPRDLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPMLEQPVAAGEM 660
            PHPKIPLPR+LYG  R NSAGLD+ANEHRLASLSSALLNSA Q W A P++E  +  G  
Sbjct: 597  PHPKIPLPRELYGEKRVNSAGLDMANEHRLASLSSALLNSASQPWIAQPLVEGALGEGVS 656

Query: 661  SPVINPAEPKDIVGYVREATPREVEQALESAVNNAPIWFATPPAERAAILHRAAVLMESQ 720
             PV+NP+ P D+VG VREA+  EV +AL++AVN  PIWFATPP ERAAIL RAA  ME Q
Sbjct: 657  RPVLNPSAPADVVGSVREASEAEVSEALDAAVNAGPIWFATPPQERAAILERAAEAMEGQ 716

Query: 721  MQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFANETHRPLGPVVCISPWNF 780
            MQQLIG+LVREAGKT++NAIAEVREAVDFL+YYAG VRDDF NETHRPLGPVVCISPWNF
Sbjct: 717  MQQLIGLLVREAGKTYNNAIAEVREAVDFLYYYAGMVRDDFDNETHRPLGPVVCISPWNF 776

Query: 781  PLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVGA 840
            PLAIF GQIAAALAAGNSVLAKPAEQTPLIAAQ + I+L+AGVP GV+QLLPG+GETVGA
Sbjct: 777  PLAIFAGQIAAALAAGNSVLAKPAEQTPLIAAQAVQIMLDAGVPAGVLQLLPGQGETVGA 836

Query: 841  QLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQGRPIPLIAETGGMNAMIVDSSALTEQ 900
            QLTGD+RVRGVMFTGST VATLLQRN+A RLD QGRP PLIAETGGMNAMIVDSSALTEQ
Sbjct: 837  QLTGDERVRGVMFTGSTAVATLLQRNLAGRLDPQGRPTPLIAETGGMNAMIVDSSALTEQ 896

Query: 901  VVVDVLASAFDSAGQRCSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVI 960
            VV+D++ASAFDSAGQRCSALR+LC+QD++ADHTLKMLRGAMAECRMGNP RL+TDIGPVI
Sbjct: 897  VVIDIVASAFDSAGQRCSALRLLCVQDDVADHTLKMLRGAMAECRMGNPERLSTDIGPVI 956

Query: 961  DSEAKANIERHIQTMRSKGRPVFQAVRENSEDAREWQSGTFVAPTLIELDDFAELQKEVF 1020
            D+EAK NI+RHIQ MR+KG  V+QA ++N +D++EW SGTF+ PTLIELD  ++L KEVF
Sbjct: 957  DAEAKDNIDRHIQAMRNKGFTVYQAAQDNPQDSKEWNSGTFIKPTLIELDQVSDLDKEVF 1016

Query: 1021 GPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVGNLYVNRNMVG 1080
            GPVLHVVR+ RN LP+LI+QINASGYGLTLGVHTRIDETIAQVT  A VGNLYVNRNMVG
Sbjct: 1017 GPVLHVVRFARNSLPQLIDQINASGYGLTLGVHTRIDETIAQVTAGAKVGNLYVNRNMVG 1076

Query: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLANRPESALAVTLARQDAKYPVDAQLKAALT 1140
            AVVGVQPFGGEGLSGTGPKAGGPLYLYRLL+NRP+ AL  T  RQDA+ PVD+ ++  L 
Sbjct: 1077 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSNRPDGALRKTFDRQDAERPVDSSVRTELM 1136

Query: 1141 QPLNALREWAANRPELQALCTQYGELAQAGTQRLLPGPTGERNTWTLLPRERVLCIADDE 1200
                AL+ WA ++P+L ALC +Y ELAQAGT R+LPGPTGERNT+TLLPRE VLCIAD+E
Sbjct: 1137 SAHQALQTWAQDKPDLLALCQRYDELAQAGTVRVLPGPTGERNTFTLLPREHVLCIADNE 1196

Query: 1201 QDALTQLAAVLAVGSQVLWPDDALHRQLVKALPSAVSERIQLAKAENITAQPFDAVIFHG 1260
            QDALTQLAAV +VGS  LW DD LHR+L   LP+AV  R+ L K  ++ A  FDAVI+HG
Sbjct: 1197 QDALTQLAAVTSVGSSALWQDDELHRELRTRLPAAVQPRVVLVK--DVLAADFDAVIYHG 1254

Query: 1261 DSDQLRALCEAVAARDGTIVSVQGFARGESNILLERLYIERSLSVNTAAAGGNASLMTIG 1320
            D+DQLR LCE VAARDG IVSVQGFARGE+N+LLERL IERSLSVNTAAAGGNASLMTIG
Sbjct: 1255 DADQLRTLCEQVAARDGAIVSVQGFARGETNLLLERLLIERSLSVNTAAAGGNASLMTIG 1314


Lambda     K      H
   0.318    0.133    0.384 

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: 4461
Number of extensions: 171
Number of successful extensions: 4
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: 1320
Length of database: 1314
Length adjustment: 48
Effective length of query: 1272
Effective length of database: 1266
Effective search space:  1610352
Effective search space used:  1610352
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_084935517.1 HA51_RS15475 (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.2446148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-251  821.6   0.4   1.1e-251  821.6   0.4    1.4  2  NCBI__GCF_002095475.1:WP_084935517.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002095475.1:WP_084935517.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  821.6   0.4  1.1e-251  1.1e-251       1     499 [.     606    1109 ..     606    1110 .. 0.99
   2 ?   -4.3   0.4      0.24      0.24     291     328 ..    1239    1278 ..    1236    1280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 821.6 bits;  conditional E-value: 1.1e-251
                             TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                            +lyge r ns+G+d+ane++l+sl++ ll++a + + a p+v e a  eg  +pv np  + d+vG v+ea
  NCBI__GCF_002095475.1:WP_084935517.1  606 ELYGEKRVNSAGLDMANEHRLASLSSALLNSASQPWIAQPLV-EGALGEGVSRPVLNPSAPADVVGSVREA 675 
                                            79****************************************.88999*********************** PP

                             TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 
                                            ++aev+ea+d+av+a ++w+at+++eraailer+a+ +e +m +l++llvreaGkt +naiaevreavdfl
  NCBI__GCF_002095475.1:WP_084935517.1  676 SEAEVSEALDAAVNAGPIWFATPPQERAAILERAAEAMEGQMQQLIGLLVREAGKTYNNAIAEVREAVDFL 746 
                                            *********************************************************************** PP

                             TIGR01238  143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213 
                                             yya+ v+d++d+e++++lG+vvcispwnfplaif GqiaaalaaGn+v+akpaeqt+liaa+av+++++a
  NCBI__GCF_002095475.1:WP_084935517.1  747 YYYAGMVRDDFDNETHRPLGPVVCISPWNFPLAIFAGQIAAALAAGNSVLAKPAEQTPLIAAQAVQIMLDA 817 
                                            *********************************************************************** PP

                             TIGR01238  214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281 
                                            Gvpagv+qllpG+Ge+vGa lt der++Gv+ftGst+va+l++++la r d++   +pliaetGG+namiv
  NCBI__GCF_002095475.1:WP_084935517.1  818 GVPAGVLQLLPGQGETVGAQLTGDERVRGVMFTGSTAVATLLQRNLAGRLDPQgrpTPLIAETGGMNAMIV 888 
                                            ***************************************************99999*************** PP

                             TIGR01238  282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352 
                                            ds+al+eqvv+d++asafdsaGqrcsalr+lcvq+dvad++l++++Gam e+++g+p+rl td+Gpvidae
  NCBI__GCF_002095475.1:WP_084935517.1  889 DSSALTEQVVIDIVASAFDSAGQRCSALRLLCVQDDVADHTLKMLRGAMAECRMGNPERLSTDIGPVIDAE 959 
                                            *********************************************************************** PP

                             TIGR01238  353 akqnllahiekmkakakkvaqvkledd...vesekgtfvaptlfelddldelkkevfGpvlhvvrykadel 420 
                                            ak+n+ +hi++m++k+ +v+q+ +++    +e++ gtf++ptl+eld++++l+kevfGpvlhvvr+ ++ l
  NCBI__GCF_002095475.1:WP_084935517.1  960 AKDNIDRHIQAMRNKGFTVYQAAQDNPqdsKEWNSGTFIKPTLIELDQVSDLDKEVFGPVLHVVRFARNSL 1030
                                            **********************9987544599*************************************** PP

                             TIGR01238  421 dkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGply 491 
                                             +++d+ina+GygltlGvh+ri+et++q++  akvGn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGply
  NCBI__GCF_002095475.1:WP_084935517.1 1031 PQLIDQINASGYGLTLGVHTRIDETIAQVTAGAKVGNLYVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLY 1101
                                            *********************************************************************** PP

                             TIGR01238  492 lyrltrvr 499 
                                            lyrl++ r
  NCBI__GCF_002095475.1:WP_084935517.1 1102 LYRLLSNR 1109
                                            ****9865 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 0.24
                             TIGR01238  291 vadvlasafdsaGqrcsa..lrvlcvqedvadrvltlikG 328 
                                            v+dvla+ fd+      a  lr lc q    d  +  ++G
  NCBI__GCF_002095475.1:WP_084935517.1 1239 VKDVLAADFDAVIYHGDAdqLRTLCEQVAARDGAIVSVQG 1278
                                            7899999999987766553377777776666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1314 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 47.88
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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