Alignments for a candidate for gatA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Caulobacter crescentus NA1000

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate CCNA_02519 CCNA_02519 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Caulo:CCNA_02519
          Length = 489

 Score =  440 bits (1132), Expect = e-128
 Identities = 229/415 (55%), Positives = 295/415 (71%), Gaps = 7/415 (1%)

Query: 67  EHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDE 126
           E G L G P+GVKD   T G+RTT  SKILENF P Y++TV  +L    AV +GKLN+D+
Sbjct: 65  EAGPLEGAPLGVKDLFCTNGVRTTACSKILENFVPTYESTVTSQLWRDGAVMLGKLNLDQ 124

Query: 127 FAMGSSTENSAYKLTKNPWNLD-----TVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
           FAMGSS E S +    NPW          PGGSSGGSAAAVAA     +  +DTGGSIRQ
Sbjct: 125 FAMGSSNETSYFGPVTNPWRAQGSTKALTPGGSSGGSAAAVAADLCLGATATDTGGSIRQ 184

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+F G VG+KPTYGR SR+G+VAFASSLDQ GPI +TVED A LL ++SG D  DSTS 
Sbjct: 185 PAAFTGTVGIKPTYGRCSRWGVVAFASSLDQAGPIAKTVEDAALLLTSMSGHDPKDSTSL 244

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
           ++ VPDF   +   +KGLKI +PKEY  + +  E  +     +  L+  G    ++SLPH
Sbjct: 245 DIPVPDFTQFVGKSVKGLKIGIPKEYRVDNMPAEIEKLWQDGIAWLKEAGCEIVDISLPH 304

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIML 361
           +KYAL  YY+++ +EAS+NLAR+DG+RYG R + A NL ++Y+ TRA GFG+EVKRRI++
Sbjct: 305 TKYALPAYYIVAPAEASSNLARYDGMRYGLREEGA-NLTEIYENTRASGFGDEVKRRILI 363

Query: 362 GTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTM 421
           GT+ LS+GYYDAYY KA KVR  I +DF++ + + D I+ PT P+ AF +GEN+ DP+ M
Sbjct: 364 GTYVLSAGYYDAYYLKALKVRRRIAEDFDNAWTQCDAILTPTAPSAAFGLGENSNDPIAM 423

Query: 422 YANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           Y ND+ T+  NLAG+PG+S+P GL A+GLPLGLQIIGK  DE+TV+ VA A E+A
Sbjct: 424 YLNDVFTVTTNLAGLPGLSLPAGLDANGLPLGLQIIGKPLDEATVFSVAGAVEKA 478


Lambda     K      H
   0.315    0.134    0.381 

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: 610
Number of extensions: 25
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: 485
Length of database: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_02519 CCNA_02519 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# 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.aa/TIGR00132.hmm
# target sequence database:        /tmp/gapView.512713.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.9e-175  567.8   0.0   1.1e-174  567.5   0.0    1.0  1  FitnessBrowser__Caulo:CCNA_02519  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_02519  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.5   0.0  1.1e-174  1.1e-174       6     463 ..      16     478 ..      12     481 .. 0.97

  Alignments for each domain:
  == domain 1  score: 567.5 bits;  conditional E-value: 1.1e-174
                         TIGR00132   6 kkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiettcaS 80 
                                        ++e++++e++++ +e+iea +  +na++  t++ka+ +a+k+d++ a  e  +l g p++vKd +++++++tt+ S
  FitnessBrowser__Caulo:CCNA_02519  16 AAREFTSVELTRAHIEAIEAARG-LNAYILETPDKAIDMAAKSDARRAlGEaGPLEGAPLGVKDLFCTNGVRTTACS 91 
                                       678899999***********999.*********************99996647************************ PP

                         TIGR00132  81 kiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGSsgGsaaavaad 152
                                       kiLen+v++y++tV+ +l ++ga+++Gk NlD FamGss etS+fg+++nP       ++  pGGSsgGsaaavaad
  FitnessBrowser__Caulo:CCNA_02519  92 KILENFVPTYESTVTSQLWRDGAVMLGKLNLDQFAMGSSNETSYFGPVTNPwraqgSTKALTPGGSSGGSAAAVAAD 168
                                       ***************************************************44333346789*************** PP

                         TIGR00132 153 lvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstsle 229
                                       l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++ak+ved+al+l  +sg+D kDstsl+
  FitnessBrowser__Caulo:CCNA_02519 169 LCLGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGVVAFASSLDQAGPIAKTVEDAALLLTSMSGHDPKDSTSLD 245
                                       ***************************************************************************** PP

                         TIGR00132 230 vkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEass 306
                                       ++v+++++ + k +kglk+g+ ke++ ++++ e+++ +++ +  l+e g+eiv++slp+ k+al++Yyi++p+Eass
  FitnessBrowser__Caulo:CCNA_02519 246 IPVPDFTQFVGKSVKGLKIGIPKEYRVDNMPAEIEKLWQDGIAWLKEAGCEIVDISLPHTKYALPAYYIVAPAEASS 322
                                       ***************************************************************************** PP

                         TIGR00132 307 nlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeev 383
                                       nlarydg+ryG r e ++ l+e+y +tR++gfg+evkrRi++G+y+ls++yyd+yy+kA kvr+ i+++f+++++++
  FitnessBrowser__Caulo:CCNA_02519 323 NLARYDGMRYGLREEGAN-LTEIYENTRASGFGDEVKRRILIGTYVLSAGYYDAYYLKALKVRRRIAEDFDNAWTQC 398
                                       *************99988.********************************************************** PP

                         TIGR00132 384 DvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakal 460
                                       D i++ptap  af lge+ +dp++myl+Dv+tv+ nlaGlp++s+P+g + +glp+Glqiigk +d+ +++sva a+
  FitnessBrowser__Caulo:CCNA_02519 399 DAILTPTAPSAAFGLGENSNDPIAMYLNDVFTVTTNLAGLPGLSLPAGLDANGLPLGLQIIGKPLDEATVFSVAGAV 475
                                       ****************************************************************************9 PP

                         TIGR00132 461 eqa 463
                                       e+a
  FitnessBrowser__Caulo:CCNA_02519 476 EKA 478
                                       987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.00
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis