Alignments for a candidate for gatA in Methylocapsa aurea KYG

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methylocapsa aurea KYG

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_036259605.1 DL86_RS06295 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000746085.1:WP_036259605.1
          Length = 496

 Score =  451 bits (1160), Expect = e-131
 Identities = 246/481 (51%), Positives = 328/481 (68%), Gaps = 11/481 (2%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L D  + E +  + KK+I   DL +    +I+     + AF+    + ARA A E D  +
Sbjct: 4   LTDLTLAEARDALAKKKISALDLANAQIAQIERAR-ALNAFVTETPDVARAMAIESDARI 62

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
             R E G L GMP+G+KD   T G++TT  S ILE F P Y++TV   L    AV +GKL
Sbjct: 63  -ARGEAGPLEGMPLGIKDLYCTAGVQTTAGSHILEGFTPAYESTVSANLWRDGAVMLGKL 121

Query: 123 NMDEFAMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGG 177
           N+DEFAMGSS E S +    +PW     N   VPGGSSGGS+AAVAA     +  +DTGG
Sbjct: 122 NLDEFAMGSSNETSYFGPVISPWRRQGANAALVPGGSSGGSSAAVAAHLCFGATATDTGG 181

Query: 178 SIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMD 237
           SIRQPA+F G VG+KPTYGR SR+G+VAFASSLDQ GPI RTV D A LL++++G D  D
Sbjct: 182 SIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARTVRDAAILLRSMAGHDPKD 241

Query: 238 STSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
           +TS NV VPD+ +++   IKG+KI +PKEY  +G+  E  +     +  ++  GA+  E+
Sbjct: 242 TTSVNVPVPDYEAAVGRSIKGMKIGIPKEYRLDGMSPEIEKLWDQGIAWMKEAGASIVEI 301

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLPH++YAL  YY+++ +EAS+NLAR+DG+RYG R    D + D+Y+ TRA GFG EV+R
Sbjct: 302 SLPHTRYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IADMYESTRAAGFGKEVRR 360

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVF-EKYDVIVGPTTPTPAFKIGE-NT 415
           RIM+GT+ LS+GYYDAYY +AQK+RTLIK+DFE  F +  D I+ P TP+ AF +GE  +
Sbjct: 361 RIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFELAFADGVDAILTPATPSAAFGLGEKGS 420

Query: 416 KDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
            DP+ MY NDI T+ VN+AG+PGI+VP G  ++GLPLGLQ+IG+ FDE T++ VA A EQ
Sbjct: 421 TDPVEMYLNDIFTVTVNMAGLPGIAVPAGTSSEGLPLGLQVIGRAFDEETLFAVAGAIEQ 480

Query: 475 A 475
           A
Sbjct: 481 A 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: 593
Number of extensions: 34
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: 496
Length adjustment: 34
Effective length of query: 451
Effective length of database: 462
Effective search space:   208362
Effective search space used:   208362
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_036259605.1 DL86_RS06295 (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.1096881.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-170  553.3   0.0   2.8e-170  553.0   0.0    1.0  1  NCBI__GCF_000746085.1:WP_036259605.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746085.1:WP_036259605.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.0   0.0  2.8e-170  2.8e-170       3     463 ..      14     481 ..      12     483 .. 0.97

  Alignments for each domain:
  == domain 1  score: 553.0 bits;  conditional E-value: 2.8e-170
                             TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 
                                           ++l kk++s+ +++++ +++ie+ +  +naf++ t++ a ++a ++d+++a  e  +l g+p+++Kd  ++ +
  NCBI__GCF_000746085.1:WP_036259605.1  14 DALAKKKISALDLANAQIAQIERARA-LNAFVTETPDVARAMAIESDARIArGEaGPLEGMPLGIKDLYCTAG 85 
                                           6789********************99.***********************975646***************** PP

                             TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....eneervpGGS 141
                                           ++tt++S+iLe++++ y++tV  +l ++ga+++Gk NlDEFamGss etS+fg++  P     +n + vpGGS
  NCBI__GCF_000746085.1:WP_036259605.1  86 VQTTAGSHILEGFTPAYESTVSANLWRDGAVMLGKLNLDEFAMGSSNETSYFGPVISPwrrqgANAALVPGGS 158
                                           **********************************************************5555557889***** PP

                             TIGR00132 142 sgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvl 214
                                           sgGs+aavaa+l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G++a++v d+a++l
  NCBI__GCF_000746085.1:WP_036259605.1 159 SGGSSAAVAAHLCFGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGIVAFASSLDQAGPIARTVRDAAILL 231
                                           ************************************************************************* PP

                             TIGR00132 215 dvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslp 287
                                             ++g+D kD+ts++v+v+++  ++ + +kg+k+g+ ke++ ++++ e+++ +++ +  ++e ga ive+slp
  NCBI__GCF_000746085.1:WP_036259605.1 232 RSMAGHDPKDTTSVNVPVPDYEAAVGRSIKGMKIGIPKEYRLDGMSPEIEKLWDQGIAWMKEAGASIVEISLP 304
                                           ************************************************************************* PP

                             TIGR00132 288 svklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydk 360
                                           + ++al++Yyi++p+Eassnlarydg+ryG rv  ++ + ++y +tR++gfg+ev+rRim+G+y+ls++yyd+
  NCBI__GCF_000746085.1:WP_036259605.1 305 HTRYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IADMYESTRAAGFGKEVRRRIMIGTYVLSAGYYDA 376
                                           *********************************9998.*********************************** PP

                             TIGR00132 361 yykkAqkvrtliidefeklf.eevDvivsptaptlafklgekaed.plemylsDvltvpanlaGlpaisvPlg 431
                                           yy +Aqk+rtli+++fe +f + vD i++p++p  af lgek +  p+emyl+D++tv++n+aGlp+i+vP+g
  NCBI__GCF_000746085.1:WP_036259605.1 377 YYVRAQKIRTLIKRDFELAFaDGVDAILTPATPSAAFGLGEKGSTdPVEMYLNDIFTVTVNMAGLPGIAVPAG 449
                                           *******************9557*****************996544*************************** PP

                             TIGR00132 432 kkekglpiGlqiigkafddkkllsvakaleqa 463
                                           ++++glp+Glq+ig+afd+++l+ va a+eqa
  NCBI__GCF_000746085.1:WP_036259605.1 450 TSSEGLPLGLQVIGRAFDEETLFAVAGAIEQA 481
                                           *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (496 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: 22.73
//
[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 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