Alignments for a candidate for gatA in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Azospirillum lipoferum B510

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012974535.1 AZL_RS10165 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000010725.1:WP_012974535.1
          Length = 493

 Score =  451 bits (1160), Expect = e-131
 Identities = 237/470 (50%), Positives = 320/470 (68%), Gaps = 12/470 (2%)

Query: 17  KKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPI 76
           KK+    +L +   + ++AV      F+    + A A AK  DE    + E G + G+PI
Sbjct: 18  KKDFTAVELAEAHVRAVEAVRP-FNIFITETPDAALAMAKASDER-RAKGEAGPMDGLPI 75

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

Query: 137 AYKLTKNPWNLDT--------VPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGV 188
               T +PW+           V GGSSGGSAA +AA     + G+DTGGSIRQPA + G 
Sbjct: 136 HQGETVSPWSPGAPGAWDRRIVAGGSSGGSAAVIAARAALGATGTDTGGSIRQPAGYTGT 195

Query: 189 VGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDF 248
           VG+KPTYGR SR+G+VA+ASSLDQ GP+TRTVED A +L+++ G D  DSTS N+ VPDF
Sbjct: 196 VGIKPTYGRCSRWGIVAYASSLDQAGPMTRTVEDAAIMLRSMCGFDPKDSTSVNLPVPDF 255

Query: 249 LSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALAT 308
            ++LTGDI+GL++ +PKEY  EG+  E        +  L+  GA   E+SLPH+KYALA 
Sbjct: 256 RAALTGDIRGLRVGIPKEYRAEGLSAEIAALWDQGIAWLKDAGAEPVEISLPHTKYALAA 315

Query: 309 YYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSS 368
           YY+++ +EAS+NLAR+DG+RYG R +   NL ++Y+ TR  GFG EV+RRI++GT+ LS+
Sbjct: 316 YYIIAPAEASSNLARYDGVRYGLRVEGG-NLKEMYENTRGAGFGPEVRRRILIGTYVLSA 374

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

Query: 429 IPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
           +PVNLAG+P +SVP GL ADGLPLGLQ+IG+ FDE T+ RV    E+A +
Sbjct: 435 VPVNLAGLPAMSVPAGLGADGLPLGLQLIGRPFDEETLLRVGQVVERAAN 484


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: 649
Number of extensions: 38
Number of successful extensions: 5
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 WP_012974535.1 AZL_RS10165 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.1210.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-172  559.0   0.0     5e-172  558.7   0.0    1.0  1  lcl|NCBI__GCF_000010725.1:WP_012974535.1  AZL_RS10165 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012974535.1  AZL_RS10165 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.7   0.0    5e-172    5e-172       5     463 ..      16     482 ..      13     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 558.7 bits;  conditional E-value: 5e-172
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l kk+++++e++e+   ++eav+  +n+f++ t++ al++ak++d++ a  e  ++ g+piavKd +++
  lcl|NCBI__GCF_000010725.1:WP_012974535.1  16 LAKKDFTAVELAEAHVRAVEAVRP-FNIFITETPDAALAMAKASDERRAkGEaGPMDGLPIAVKDLFCT 83 
                                               67899999**************99.*********************99865546*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP........e 132
                                               k++ tt++S+iL+++++ y++tV+ +l ++ga+++Gk NlDEFamGs+t t   g t  P        +
  lcl|NCBI__GCF_000010725.1:WP_012974535.1  84 KGVATTAGSRILDGFKPEYESTVTSQLWRDGAVMLGKVNLDEFAMGSATITAHQGETVSPwspgapgaW 152
                                               ************************************************************999999999 PP

                                 TIGR00132 133 neervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG 201
                                               +++ v+GGSsgGsaa++aa  +  a g+DTGgSiRqPA ++g+vG+KPtYG+ SR+G+vayasSldq G
  lcl|NCBI__GCF_000010725.1:WP_012974535.1 153 DRRIVAGGSSGGSAAVIAARAALGATGTDTGGSIRQPAGYTGTVGIKPTYGRCSRWGIVAYASSLDQAG 221
                                               ********************************************************************* PP

                                 TIGR00132 202 ilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekl 270
                                               +++++ved+a++l  ++g D kDsts++ +v+++  +l+ d++gl+vg+ ke++ e+l+ e+++ +++ 
  lcl|NCBI__GCF_000010725.1:WP_012974535.1 222 PMTRTVEDAAIMLRSMCGFDPKDSTSVNLPVPDFRAALTGDIRGLRVGIPKEYRAEGLSAEIAALWDQG 290
                                               ********************************************************************* PP

                                 TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfg 339
                                               +  l++ gae ve+slp+ k+ala+Yyii+p+Eassnlarydg+ryG rve  + lke+y +tR +gfg
  lcl|NCBI__GCF_000010725.1:WP_012974535.1 291 IAWLKDAGAEPVEISLPHTKYALAAYYIIAPAEASSNLARYDGVRYGLRVEGGN-LKEMYENTRGAGFG 358
                                               ***************************************************999.************** PP

                                 TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplem 408
                                                ev+rRi++G+y+ls++yyd+yy+kA +vrt i+++f+++f+++Dvi++ptap ++f +gek++dp++m
  lcl|NCBI__GCF_000010725.1:WP_012974535.1 359 PEVRRRILIGTYVLSAGYYDAYYNKARQVRTRIKQDFDEAFKSCDVILTPTAPSTPFAIGEKMDDPVQM 427
                                               ********************************************************************* PP

                                 TIGR00132 409 ylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               yl Dv+tvp+nlaGlpa+svP+g   +glp+Glq+ig+ fd+++ll+v++ +e+a
  lcl|NCBI__GCF_000010725.1:WP_012974535.1 428 YLIDVFTVPVNLAGLPAMSVPAGLGADGLPLGLQLIGRPFDEETLLRVGQVVERA 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.27
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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