Alignments for a candidate for gatA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Azospirillum brasilense Sp245

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate AZOBR_RS20645 AZOBR_RS20645 glutamyl-tRNA(Gln) amidotransferase

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__azobra:AZOBR_RS20645
          Length = 493

 Score =  462 bits (1190), Expect = e-135
 Identities = 244/468 (52%), Positives = 328/468 (70%), Gaps = 12/468 (2%)

Query: 17  KKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPI 76
           KKE    +L +   K ++ +   + AF+    E+A A AK  D A   + E G + G+PI
Sbjct: 18  KKEFTAVELTEAHVKAVETIRP-LNAFITETPEQALAMAKASD-ARRAKGEAGPMEGLPI 75

Query: 77  GVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENS 136
            VKD   TKG+ TT +S IL+ F P Y++TV   L    AV +GK+N+DEFAMGS+   S
Sbjct: 76  AVKDLFCTKGVPTTAASHILDGFKPEYESTVTSNLWRDGAVMLGKVNLDEFAMGSANITS 135

Query: 137 AYKLTKNPWN--------LDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGV 188
            +    +PW+           VPGGSSGGSAAAVAA     + G+DTGGSIRQPA+F G+
Sbjct: 136 HHGNVISPWSPGEVGNWSRQIVPGGSSGGSAAAVAARAALGATGTDTGGSIRQPAAFTGI 195

Query: 189 VGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDF 248
           VG+KPTYGR SR+G+VAFASSLDQ GP+TRTVED A +L+++ G D  DSTS ++ VPDF
Sbjct: 196 VGIKPTYGRCSRWGVVAFASSLDQAGPMTRTVEDAAIMLRSMCGFDPKDSTSVDLPVPDF 255

Query: 249 LSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALAT 308
            ++LTGDI+GLK+ +PKEY  EG+  E        ++ L+  GA   E+SLPH+KYALAT
Sbjct: 256 RAALTGDIRGLKVGIPKEYRVEGMPAEIAAIWDQGIEWLKQAGAEPVEISLPHTKYALAT 315

Query: 309 YYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSS 368
           YY+++ +EAS+NLAR+DG+RYG R + A +L D+Y+ TR  GFG EV+RRI++GT+ LS+
Sbjct: 316 YYIVAPAEASSNLARYDGLRYGLRVEGA-SLKDMYENTRGAGFGKEVRRRILIGTYVLSA 374

Query: 369 GYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILT 428
           GYYDAYY KA++VRT IK DF++ F++ DVI+ PT P+ AF IGE   DP+ MY ND+ T
Sbjct: 375 GYYDAYYNKARQVRTRIKWDFDEAFKQCDVILTPTAPSTAFAIGEKMDDPIQMYLNDVFT 434

Query: 429 IPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           +P +LAG+PG+SVP G+ +DGLPLGLQ++G+ FDE TV RV    E+A
Sbjct: 435 VPASLAGLPGMSVPAGVGSDGLPLGLQLLGRPFDEETVLRVGQVIEKA 482


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: 669
Number of extensions: 36
Number of successful extensions: 6
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: 493
Length adjustment: 34
Effective length of query: 451
Effective length of database: 459
Effective search space:   207009
Effective search space used:   207009
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 AZOBR_RS20645 AZOBR_RS20645 (glutamyl-tRNA(Gln) amidotransferase)
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.16143.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-174  566.9   0.0   2.1e-174  566.6   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS20645  AZOBR_RS20645 glutamyl-tRNA(Gln)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS20645  AZOBR_RS20645 glutamyl-tRNA(Gln) amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.6   0.0  2.1e-174  2.1e-174       5     463 ..      16     482 ..      13     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 566.6 bits;  conditional E-value: 2.1e-174
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l kke++++e++e+  +++e+++  +naf++ t+e+al++ak++d++ a  e  ++ g+piavKd +++
  lcl|FitnessBrowser__azobra:AZOBR_RS20645  16 LAKKEFTAVELTEAHVKAVETIRP-LNAFITETPEQALAMAKASDARRAkGEaGPMEGLPIAVKDLFCT 83 
                                               67999******************9.********************998865546*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP........e 132
                                               k+++tt+aS+iL+++++ y++tV+ +l ++ga+++Gk NlDEFamGs+  tS +g +  P        +
  lcl|FitnessBrowser__azobra:AZOBR_RS20645  84 KGVPTTAASHILDGFKPEYESTVTSNLWRDGAVMLGKVNLDEFAMGSANITSHHGNVISPwspgevgnW 152
                                               ************************************************************888999988 PP

                                 TIGR00132 133 neervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG 201
                                                ++ vpGGSsgGsaaavaa  +  a g+DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G
  lcl|FitnessBrowser__azobra:AZOBR_RS20645 153 SRQIVPGGSSGGSAAAVAARAALGATGTDTGGSIRQPAAFTGIVGIKPTYGRCSRWGVVAFASSLDQAG 221
                                               999****************************************************************** PP

                                 TIGR00132 202 ilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekl 270
                                               +++++ved+a++l  ++g D kDsts++ +v+++  +l+ d++glkvg+ ke++ e+++ e+++ +++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS20645 222 PMTRTVEDAAIMLRSMCGFDPKDSTSVDLPVPDFRAALTGDIRGLKVGIPKEYRVEGMPAEIAAIWDQG 290
                                               ********************************************************************* PP

                                 TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfg 339
                                               +e l++ gae ve+slp+ k+ala+Yyi++p+Eassnlarydg+ryG rve ++ lk++y +tR +gfg
  lcl|FitnessBrowser__azobra:AZOBR_RS20645 291 IEWLKQAGAEPVEISLPHTKYALATYYIVAPAEASSNLARYDGLRYGLRVEGAS-LKDMYENTRGAGFG 358
                                               **************************************************9988.************** PP

                                 TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplem 408
                                               +ev+rRi++G+y+ls++yyd+yy+kA +vrt i+ +f+++f+++Dvi++ptap +af +gek++dp++m
  lcl|FitnessBrowser__azobra:AZOBR_RS20645 359 KEVRRRILIGTYVLSAGYYDAYYNKARQVRTRIKWDFDEAFKQCDVILTPTAPSTAFAIGEKMDDPIQM 427
                                               ********************************************************************* PP

                                 TIGR00132 409 ylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               yl+Dv+tvpa+laGlp++svP+g+ ++glp+Glq+ g+ fd++++l+v++ +e+a
  lcl|FitnessBrowser__azobra:AZOBR_RS20645 428 YLNDVFTVPASLAGLPGMSVPAGVGSDGLPLGLQLLGRPFDEETVLRVGQVIEKA 482
                                               ***************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (493 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: 00:00:00.02
# Mc/sec: 10.85
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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 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