GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Novosphingobium fuchskuhlense FNE08-7

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_067912680.1 AQZ52_RS14875 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>NCBI__GCF_001519075.1:WP_067912680.1
          Length = 1205

 Score = 1409 bits (3648), Expect = 0.0
 Identities = 771/1226 (62%), Positives = 899/1226 (73%), Gaps = 38/1226 (3%)

Query: 21   FAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITALRAKPR 80
            FAP I P T LR AIT A R PEP+ +  L   A+LP       AATAR LI ALRAK R
Sbjct: 7    FAPRISPETPLRRAITQATRIPEPDAVRPLLAAATLPEADRARIAATARALIEALRAKAR 66

Query: 81   GRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLGKGGSM 140
               V+ L+ E++LSS EG+ALMCLAEALLRIPD ATRDALIRDK++ G+W AHLG+G  +
Sbjct: 67   PGRVQALVQEFALSSHEGVALMCLAEALLRIPDDATRDALIRDKLSTGNWAAHLGQGKPL 126

Query: 141  FVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQFVTGQT 200
            FVNAATWGL+ITGKLT++     L  ALTR++ R GEP+IRRGVD A+RMMGEQFV G+T
Sbjct: 127  FVNAATWGLVITGKLTASVDATGLGHALTRMVHRLGEPVIRRGVDVALRMMGEQFVMGET 186

Query: 201  IQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGT----ASAGRGV 256
            I++AL  AR  EA+GF +SYDMLGEAA TA+DAARY   Y  AIHAIG     ASAGRGV
Sbjct: 187  IEDALARARRREAQGFAFSYDMLGEAAATAQDAARYLEAYTAAIHAIGQSANRASAGRGV 246

Query: 257  YEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLELS 316
            + GPGISIKLSA+HPRY+RAQA RVM EL PRV ALA LAK YDI  NIDAEE DRLELS
Sbjct: 247  FAGPGISIKLSALHPRYTRAQAHRVMAELAPRVLALAELAKSYDIDFNIDAEETDRLELS 306

Query: 317  LDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWDS 376
            LD++E L   P LAGW G+GFV+QAY KRCP VID+++DLAR SG R+M+RLVKGAYWD+
Sbjct: 307  LDILERLAHAPVLAGWQGLGFVIQAYQKRCPAVIDWIVDLARSSGRRIMVRLVKGAYWDA 366

Query: 377  EIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMAG 436
            EIKRAQ  GL DFPVYTRKV+TD++YVACARKLLAA +AVFPQFATHNAQTLA++  +AG
Sbjct: 367  EIKRAQEAGLSDFPVYTRKVHTDLAYVACARKLLAARDAVFPQFATHNAQTLASVLHLAG 426

Query: 437  SDFQVGKYEFQCLHGMGEPLYKEVVGP--LKRPCRIYAPVGTHETLLAYLVRRLLENGAN 494
             DF  G YEFQCLHGMGEPLY+EVVGP  L RPCR+YAPVGTHETLLAYLVRRLLENGAN
Sbjct: 427  PDFTPGDYEFQCLHGMGEPLYEEVVGPEGLDRPCRVYAPVGTHETLLAYLVRRLLENGAN 486

Query: 495  SSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSDE 554
            SSFVNRIADP VPV+ L+ DP AV  A    GAPH  IALP+ L+A +RAN+ G+DL+DE
Sbjct: 487  SSFVNRIADPDVPVEALIEDPAAVIAAEPEPGAPHDAIALPQALFA-DRANAQGLDLADE 545

Query: 555  TELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAEA 614
              LA L+ ALS SA     A      G+ A  A+PVRNPAD RD+VG V  A+    A A
Sbjct: 546  PTLAALAEALSGSAAQDHRA------GDPARPAEPVRNPADHRDIVGHVHAATIEDAARA 599

Query: 615  FGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREAI 674
               A AAAS W+ATP E RAA+L RAAD M+     L+ L++REAGKS  NA+AEVREA+
Sbjct: 600  A--ADAAASRWSATPAEARAAALERAADAMEAARVPLIALLIREAGKSAANALAEVREAV 657

Query: 675  DFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEET 734
            DFLRYY  Q R   + A  +PLGPV CISPWNFPLAIF+GQIAAALAAGNPVLAKPA ET
Sbjct: 658  DFLRYYAVQARHLPETA--QPLGPVACISPWNFPLAIFTGQIAAALAAGNPVLAKPAPET 715

Query: 735  PLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQLA 794
            PL+AAEAVR+LHA GIPA AL LLPG G++GAALV    V+GV+FTGST  AR IQ+ LA
Sbjct: 716  PLVAAEAVRLLHATGIPAAALHLLPGGGKIGAALVAAPEVQGVVFTGSTMTARAIQQSLA 775

Query: 795  GRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQED 854
            GRL   GA IPLIAETGG NAM+VDSSAL EQVV DV+ASAFDSAGQRCSALR+LCLQ+D
Sbjct: 776  GRLNAHGATIPLIAETGGLNAMVVDSSALPEQVVADVLASAFDSAGQRCSALRLLCLQDD 835

Query: 855  VADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLP 914
            +ADRTL+MLK AM EL  GNP +LA DVGPVISE ARA IAAH+  MRA G  V  +PL 
Sbjct: 836  IADRTLSMLKAAMAELAGGNPAQLATDVGPVISERARAGIAAHVARMRAAGFPVTEMPLG 895

Query: 915  AETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLH 974
             +TA GTF+APT+IE+    +L  EVFGPVLHVVRF  + +D+L++ INA+GYGLTFGLH
Sbjct: 896  EQTAHGTFVAPTLIELNTPTDLTAEVFGPVLHVVRFRAEAIDSLIEGINASGYGLTFGLH 955

Query: 975  TRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSRR 1034
            TRID T+ERV GRI AGN+YVNRN IGAVVGVQPFGG GLSGTGPKAGGPLYL+R     
Sbjct: 956  TRIDQTVERVCGRIEAGNLYVNRNMIGAVVGVQPFGGRGLSGTGPKAGGPLYLARFAPGA 1015

Query: 1035 PKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNGPVGERNL 1094
                 +   P     A  A+ +W   +G  A A         S +G  A L GPVGERN 
Sbjct: 1016 VPVLPQGDYPAVPDPALAAFAQWASQQGLAAAAQTAWNAAKASPLGFTATLPGPVGERNT 1075

Query: 1095 YELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVRTTA 1154
            Y L  RGR+         L  Q+ AVLATGN+A + AP  +A    G PPALAARV    
Sbjct: 1076 YRLAPRGRIACAATGVEALWQQVAAVLATGNTAVIVAPSPVAARPAGFPPALAARV---- 1131

Query: 1155 DWRD-----VGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDL 1209
            +W D     V  LAA+L++G  +R+   +R++A     I+ +   T             L
Sbjct: 1132 EWSDEHLTRVPDLAAMLIDGPADRIAEASRQLAAREHAIVPLHTGT------------PL 1179

Query: 1210 DLLLNERSVSVNTAAAGGNASLVAMS 1235
             LLL E ++SVNT AAGGNASL+A++
Sbjct: 1180 HLLLEEVTLSVNTTAAGGNASLMALA 1205


Lambda     K      H
   0.319    0.136    0.396 

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: 3939
Number of extensions: 182
Number of successful extensions: 12
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: 1235
Length of database: 1205
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1158
Effective search space:  1375704
Effective search space used:  1375704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

Align candidate WP_067912680.1 AQZ52_RS14875 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
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.2726782.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-200  652.3   5.6   2.2e-200  652.3   5.6    1.5  2  NCBI__GCF_001519075.1:WP_067912680.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001519075.1:WP_067912680.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.3   5.6  2.2e-200  2.2e-200       2     495 ..     530    1011 ..     529    1014 .. 0.97
   2 ?   -3.7   0.1      0.17      0.17     180     195 ..    1097    1113 ..    1093    1168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 652.3 bits;  conditional E-value: 2.2e-200
                             TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72  
                                            l+++ r n++G+dla e +l+ l e l  +aa++++a             a+pv+npad++divG+v+ a 
  NCBI__GCF_001519075.1:WP_067912680.1  530 LFAD-RANAQGLDLADEPTLAALAEALSGSAAQDHRAGDPA-------RPAEPVRNPADHRDIVGHVHAAT 592 
                                            7888.******************************997544.......679*****************999 PP

                             TIGR01238   73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143 
                                             +++ +a  +a aa++ wsat+a+ raa ler+ad +e     l+all+reaGk+  na+aevreavdflr
  NCBI__GCF_001519075.1:WP_067912680.1  593 IEDAARA--AADAAASRWSATPAEARAAALERAADAMEAARVPLIALLIREAGKSAANALAEVREAVDFLR 661 
                                            8876655..6778899******************************************************* PP

                             TIGR01238  144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214 
                                            yya q+++ l+e  a++lG+v cispwnfplaiftGqiaaalaaGn v+akpa +t+l+aa+av ll+ +G
  NCBI__GCF_001519075.1:WP_067912680.1  662 YYAVQARH-LPET-AQPLGPVACISPWNFPLAIFTGQIAAALAAGNPVLAKPAPETPLVAAEAVRLLHATG 730 
                                            ******65.7776.9******************************************************** PP

                             TIGR01238  215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282 
                                            +pa+++ llpG G+ +Gaal + + ++Gv+ftGst +ar i+++la r +a+   +pliaetGG nam+vd
  NCBI__GCF_001519075.1:WP_067912680.1  731 IPAAALHLLPGGGK-IGAALVAAPEVQGVVFTGSTMTARAIQQSLAGRLNAHgatIPLIAETGGLNAMVVD 800 
                                            ***********999.**********************************9988889*************** PP

                             TIGR01238  283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353 
                                            s+al+eqvvadvlasafdsaGqrcsalr+lc+q+d+adr+l+++k am el  g+p +l tdvGpvi ++a
  NCBI__GCF_001519075.1:WP_067912680.1  801 SSALPEQVVADVLASAFDSAGQRCSALRLLCLQDDIADRTLSMLKAAMAELAGGNPAQLATDVGPVISERA 871 
                                            *********************************************************************** PP

                             TIGR01238  354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 
                                            +  + ah+ +m+a +  v+++ l +  ++ +gtfvaptl+el+   +l  evfGpvlhvvr++a+ +d+++
  NCBI__GCF_001519075.1:WP_067912680.1  872 RAGIAAHVARMRAAGFPVTEMPLGE--QTAHGTFVAPTLIELNTPTDLTAEVFGPVLHVVRFRAEAIDSLI 940 
                                            ***********************99..899***************************************** PP

                             TIGR01238  425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495 
                                            + ina+Gyglt+G+h+ri++tv ++ +r+++Gn+yvnrn++GavvGvqpfGG+GlsGtGpkaGGplyl r+
  NCBI__GCF_001519075.1:WP_067912680.1  941 EGINASGYGLTFGLHTRIDQTVERVCGRIEAGNLYVNRNMIGAVVGVQPFGGRGLSGTGPKAGGPLYLARF 1011
                                            *********************************************************************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.17
                             TIGR01238  180 qiaaalaaGnt.viakp 195 
                                            q+aa la+Gnt vi  p
  NCBI__GCF_001519075.1:WP_067912680.1 1097 QVAAVLATGNTaVIVAP 1113
                                            67777777776334333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1205 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: 34.71
//
[ok]

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

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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:

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