Alignments for a candidate for gatA in Methyloferula stellata AR4T

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methyloferula stellata AR4T

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_020175309.1 A3OQ_RS0110315 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000385335.1:WP_020175309.1
          Length = 493

 Score =  443 bits (1140), Expect = e-129
 Identities = 242/481 (50%), Positives = 326/481 (67%), Gaps = 11/481 (2%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L D  +   +  + +K+I   DL       I+     + AF+    E A A A + DE +
Sbjct: 4   LTDLTLAGARDALKQKQISAVDLAKAHIDAIEKAR-ALNAFIVETPELALAAAAQSDEKL 62

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
             + E   L G+P+G+KD   TKG++TT  S +LE F P Y++TV   L    A  +GKL
Sbjct: 63  -AKGEARPLEGLPLGIKDLYCTKGVQTTAGSHMLEGFVPPYESTVSSNLLRDGANMLGKL 121

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNL--DT---VPGGSSGGSAAAVAAGEVPFSLGSDTGG 177
           NMDEFAMGSS E S +    +PW    DT    PGGSSGGSAAAVAA     +  SDTGG
Sbjct: 122 NMDEFAMGSSNETSYFGPVVSPWRRAGDTKPLTPGGSSGGSAAAVAAHLCLAATASDTGG 181

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

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

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

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGE-NT 415
           RIM+GT+ LS+GYYDAYY +AQK+RTLIK+DFE VFEK  D I+ P TP+ AF +GE ++
Sbjct: 361 RIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFETVFEKGIDAILTPATPSAAFGLGEKSS 420

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

Query: 475 A 475
           +
Sbjct: 481 S 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: 605
Number of extensions: 37
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 WP_020175309.1 A3OQ_RS0110315 (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.17296.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-173  561.5   0.0   9.1e-173  561.2   0.0    1.0  1  lcl|NCBI__GCF_000385335.1:WP_020175309.1  A3OQ_RS0110315 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000385335.1:WP_020175309.1  A3OQ_RS0110315 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 !  561.2   0.0  9.1e-173  9.1e-173       2     463 ..      13     481 ..      12     483 .. 0.96

  Alignments for each domain:
  == domain 1  score: 561.2 bits;  conditional E-value: 9.1e-173
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                               +++lk+k++s+++++++ +++ie+ +  +naf+  t+e al++a+++d+k+a  e ++l g+p+++Kd 
  lcl|NCBI__GCF_000385335.1:WP_020175309.1  13 RDALKQKQISAVDLAKAHIDAIEKARA-LNAFIVETPELALAAAAQSDEKLAkGEaRPLEGLPLGIKDL 80 
                                               57899*******************999.**********************9965546************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPenee.. 135
                                                ++k+++tt++S++Le++v+py++tV  +l ++ga ++Gk N+DEFamGss etS+fg++  P+ ++  
  lcl|NCBI__GCF_000385335.1:WP_020175309.1  81 YCTKGVQTTAGSHMLEGFVPPYESTVSSNLLRDGANMLGKLNMDEFAMGSSNETSYFGPVVSPWRRAgd 149
                                               ***************************************************************754322 PP

                                 TIGR00132 136 ...rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG 201
                                                    pGGSsgGsaaavaa+l+  a +sDTGgSiRqPA+f+g+vG+KPtYG+ SR+G+va+asSldq G
  lcl|NCBI__GCF_000385335.1:WP_020175309.1 150 tkpLTPGGSSGGSAAAVAAHLCLAATASDTGGSIRQPAAFTGTVGIKPTYGRCSRWGMVAFASSLDQAG 218
                                               22279**************************************************************** PP

                                 TIGR00132 202 ilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekl 270
                                               ++a++v d+a++l  ++g+D+kD+ts++ +v+++ ++l + +kg+k+g+ ke++ ++++ e+++ +++ 
  lcl|NCBI__GCF_000385335.1:WP_020175309.1 219 PIARTVRDTAIMLRSMAGVDAKDTTSVDLPVPDYETALGRSIKGMKIGIPKEYRIDGMPAEIENLWQQG 287
                                               ********************************************************************* PP

                                 TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfg 339
                                               +e +++ gaeiv++slp+ ++al++Yyi++p+Eassnlarydg+ryG rv  ++ +  +y +tR++gfg
  lcl|NCBI__GCF_000385335.1:WP_020175309.1 288 IEWMKAAGAEIVDISLPHTRYALPAYYIVAPAEASSNLARYDGVRYGLRVPGKD-IASMYENTRAAGFG 355
                                               **************************************************9998.************** PP

                                 TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfee.vDvivsptaptlafklgekaed.pl 406
                                               +ev+rRim+G+y+ls++yyd+yy +Aqk+rtli+++fe +fe+ +D i++p++p  af lgek +  p+
  lcl|NCBI__GCF_000385335.1:WP_020175309.1 356 KEVRRRIMIGTYVLSAGYYDAYYVRAQKIRTLIKRDFETVFEKgIDAILTPATPSAAFGLGEKSSAdPI 424
                                               *****************************************7549****************998655** PP

                                 TIGR00132 407 emylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               emyl+D++tv++n+aGlp+i+vP+g +++glp+Glq+ig+afd+++l+sva  +eq 
  lcl|NCBI__GCF_000385335.1:WP_020175309.1 425 EMYLNDIFTVTVNMAGLPGIAVPAGLSSEGLPLGLQLIGRAFDEETLFSVADVIEQS 481
                                               ****************************************************99985 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: 10.50
//
[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