Alignments for a candidate for gatA in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Bradyrhizobium sp. BTAi1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012044724.1 BBTA_RS22065 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000015165.1:WP_012044724.1
          Length = 491

 Score =  442 bits (1136), Expect = e-128
 Identities = 239/476 (50%), Positives = 323/476 (67%), Gaps = 11/476 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + E ++ +  K     +L D   K ++     + AF+    ++ARA A+E D  + G+ E
Sbjct: 9   LAEARKGLASKTFTSLELTDAHLKAMEEAR-ALNAFVMETPDQARAMAREADARI-GKGE 66

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+P+G+KD   TK +RTT  SKIL NF P Y++TV  +L    AV +GKLN DEF
Sbjct: 67  AGPLAGIPLGIKDLFATKDVRTTACSKILGNFVPTYESTVTSQLWRDGAVMLGKLNNDEF 126

Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           AMGSS E S +    NPW     N   VPGGSSGGSA+AVAA     +  +DTGGSIRQP
Sbjct: 127 AMGSSNETSCFGPVGNPWRREGSNTTLVPGGSSGGSASAVAALLCMGATATDTGGSIRQP 186

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           A+F   VG+KPTYGR SR+G+VAFASSLDQ GPI R+  D A LL++++G D  D+TS +
Sbjct: 187 AAFTATVGIKPTYGRCSRWGIVAFASSLDQAGPIARSTRDAAILLRSMAGHDPKDTTSVD 246

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
           + VPD+ +++   +KG+KI +P+EY  +G+  E  +        L+  GA   EVSLPH+
Sbjct: 247 IPVPDYEAAIGRSVKGMKIGIPREYRLDGMPAEIEKLWSDGADWLKAAGAELVEVSLPHT 306

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           KYAL  YY+++ +EAS+NLAR+DG+RYG R  +  ++ +LY+ TRAEGFG EV+RR+M+G
Sbjct: 307 KYALPAYYIVAPAEASSNLARYDGVRYGLRV-SGKSIGELYENTRAEGFGPEVRRRVMIG 365

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGE-NTKDPLT 420
           T+ LS+GYYDAYY +AQKVRTLIK+DFED F K  + I+ P TP+ AF IGE    DP+ 
Sbjct: 366 TYVLSAGYYDAYYIRAQKVRTLIKRDFEDCFAKGVNAILTPATPSAAFGIGEKGGADPVE 425

Query: 421 MYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           MY NDI T+ VN+AG+PGI+VP G  + GLPLGLQ+IG+ FDE T++ +    EQA
Sbjct: 426 MYLNDIFTVTVNMAGLPGIAVPAGKDSQGLPLGLQLIGRPFDEETLFSLGEVIEQA 481


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: 598
Number of extensions: 32
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: 491
Length adjustment: 34
Effective length of query: 451
Effective length of database: 457
Effective search space:   206107
Effective search space used:   206107
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_012044724.1 BBTA_RS22065 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB 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.11294.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-167  544.1   0.0   1.5e-167  543.9   0.0    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012044724.1  BBTA_RS22065 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012044724.1  BBTA_RS22065 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.9   0.0  1.5e-167  1.5e-167       5     463 ..      16     481 ..      12     484 .. 0.96

  Alignments for each domain:
  == domain 1  score: 543.9 bits;  conditional E-value: 1.5e-167
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l +k++++ e++++ l+++e+ +  +naf+  t+++a ++a++ d+++   e  +lagip+++Kd +a+
  lcl|NCBI__GCF_000015165.1:WP_012044724.1  16 LASKTFTSLELTDAHLKAMEEARA-LNAFVMETPDQARAMAREADARIGkGEaGPLAGIPLGIKDLFAT 83 
                                               567888889999999999999998.***********************865546*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....enee 135
                                               kd++tt+ SkiL n+v++y++tV+ +l ++ga+++Gk N DEFamGss etS+fg++ nP      n++
  lcl|NCBI__GCF_000015165.1:WP_012044724.1  84 KDVRTTACSKILGNFVPTYESTVTSQLWRDGAVMLGKLNNDEFAMGSSNETSCFGPVGNPwrregSNTT 152
                                               ************************************************************555555889 PP

                                 TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                                vpGGSsgGsa avaa l+  a ++DTGgSiRqPA+f+++vG+KPtYG+ SR+G+va+asSldq G++a
  lcl|NCBI__GCF_000015165.1:WP_012044724.1 153 LVPGGSSGGSASAVAALLCMGATATDTGGSIRQPAAFTATVGIKPTYGRCSRWGIVAFASSLDQAGPIA 221
                                               9******************************************************************** PP

                                 TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllek 273
                                               ++  d+a++l  ++g+D kD+ts++++v+++  ++ + +kg+k+g+ +e++ ++++ e+++ + +  + 
  lcl|NCBI__GCF_000015165.1:WP_012044724.1 222 RSTRDAAILLRSMAGHDPKDTTSVDIPVPDYEAAIGRSVKGMKIGIPREYRLDGMPAEIEKLWSDGADW 290
                                               ********************************************************************* PP

                                 TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342
                                               l++ gae+vevslp+ k+al++Yyi++p+Eassnlarydg+ryG rv+ ++ + ely +tR+egfg ev
  lcl|NCBI__GCF_000015165.1:WP_012044724.1 291 LKAAGAELVEVSLPHTKYALPAYYIVAPAEASSNLARYDGVRYGLRVSGKS-IGELYENTRAEGFGPEV 358
                                               ***********************************************9988.***************** PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklf.eevDvivsptaptlafklgeka.edplemy 409
                                               +rR+m+G+y+ls++yyd+yy++Aqkvrtli+++fe+ f + v  i++p++p  af +gek  +dp+emy
  lcl|NCBI__GCF_000015165.1:WP_012044724.1 359 RRRVMIGTYVLSAGYYDAYYIRAQKVRTLIKRDFEDCFaKGVNAILTPATPSAAFGIGEKGgADPVEMY 427
                                               **************************************567******************96256***** PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               l+D++tv++n+aGlp+i+vP+gk+++glp+Glq+ig+ fd+++l+s+++ +eqa
  lcl|NCBI__GCF_000015165.1:WP_012044724.1 428 LNDIFTVTVNMAGLPGIAVPAGKDSQGLPLGLQLIGRPFDEETLFSLGEVIEQA 481
                                               ***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (491 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.04
//
[ok]

This GapMind analysis is from Apr 10 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