Alignments for a candidate for gatA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Magnetospirillum magneticum AMB-1

Align glutamyl-tRNA^Gln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate WP_043743836.1 AMB_RS07995 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= metacyc::MONOMER-13955
         (485 letters)



>NCBI__GCF_000009985.1:WP_043743836.1
          Length = 490

 Score =  477 bits (1228), Expect = e-139
 Identities = 255/489 (52%), Positives = 338/489 (69%), Gaps = 11/489 (2%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L D  + E +  + K      +L D   K  +A    + AF+    + A   AK  D   
Sbjct: 4   LTDLTMAEARDGLAKGAFTAVELTDAHIKATEA-QRHLNAFIVETPDLALEAAKASDARR 62

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
              +  G + G+PIG+KD   T+G++TT +S ILE F P Y++TV  +L+ A A+++GKL
Sbjct: 63  QAGTA-GSMDGLPIGIKDLFCTEGVQTTAASHILEGFKPPYESTVSGKLKAAGAISLGKL 121

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDT------VPGGSSGGSAAAVAAGEVPFSLGSDTG 176
           N+DEFAMGSS + S +   +NPW   +      VPGGSSGGSAAAVAA  V  + G+DTG
Sbjct: 122 NLDEFAMGSSNQTSYFGAVENPWKKTSDPKAKLVPGGSSGGSAAAVAARMVLGATGTDTG 181

Query: 177 GSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKM 236
           GSIRQPA+FCG+ G+KPTYGR SR+G+VAFASSLDQ GP+ RTV D A +L A++G D  
Sbjct: 182 GSIRQPAAFCGITGIKPTYGRCSRFGIVAFASSLDQAGPMARTVRDCAIMLGAMAGHDPK 241

Query: 237 DSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEE 296
           DSTS N+ VPDF  +LTGDI+GLK+ +PKEY  +G+  E  +     ++ L+  GAT  E
Sbjct: 242 DSTSVNMAVPDFERALTGDIRGLKVGIPKEYRPDGLSDEVAKVWDRGIEWLKAAGATPVE 301

Query: 297 VSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVK 356
           +SLPH+KYALATYY+++ +E S+NLAR+DG+RYG R      L D+YK++RA GFG EV+
Sbjct: 302 ISLPHTKYALATYYIIAPAECSSNLARYDGLRYGLRVP-GKTLDDMYKKSRAAGFGAEVR 360

Query: 357 RRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTK 416
           RRI++GT+ LS+GYYDAYY KAQKVR LI +DF   FE  DVI+ PT P+ AF +GE T 
Sbjct: 361 RRILIGTYVLSAGYYDAYYAKAQKVRRLIAEDFRKAFETVDVILTPTAPSAAFGMGEGTD 420

Query: 417 DPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           DP+TM+ ND+ TIP ++AG+PG+S+P GL ADGLPLGLQ+IG+ FDE TV+RVA   E A
Sbjct: 421 DPVTMWLNDVFTIPTSMAGLPGLSLPAGLSADGLPLGLQLIGRPFDEETVFRVAGVMETA 480

Query: 476 TDHHKAKPE 484
             +  AKPE
Sbjct: 481 A-NFTAKPE 488


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: 613
Number of extensions: 33
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: 490
Length adjustment: 34
Effective length of query: 451
Effective length of database: 456
Effective search space:   205656
Effective search space used:   205656
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_043743836.1 AMB_RS07995 (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.369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-175  568.4   0.0   6.7e-175  568.2   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043743836.1  AMB_RS07995 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743836.1  AMB_RS07995 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 !  568.2   0.0  6.7e-175  6.7e-175       6     463 ..      17     480 ..      12     483 .. 0.96

  Alignments for each domain:
  == domain 1  score: 568.2 bits;  conditional E-value: 6.7e-175
                                 TIGR00132   6 kkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 
                                                k  ++++e++++ +++ ea+++ +naf+  t++ al++ak++d++ +  +   + g+pi++Kd ++++
  lcl|NCBI__GCF_000009985.1:WP_043743836.1  17 AKGAFTAVELTDAHIKATEAQRH-LNAFIVETPDLALEAAKASDARRQaGTaGSMDGLPIGIKDLFCTE 84 
                                               56677888888999998888887.********************9988655369*************** PP

                                 TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPene......e 135
                                               +++tt+aS+iLe++++py++tV  +lk+aga+ +Gk NlDEFamGss +tS+fg+++nP+++      +
  lcl|NCBI__GCF_000009985.1:WP_043743836.1  85 GVQTTAASHILEGFKPPYESTVSGKLKAAGAISLGKLNLDEFAMGSSNQTSYFGAVENPWKKtsdpkaK 153
                                               ***********************************************************8762222226 PP

                                 TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                                vpGGSsgGsaaavaa +v  a g+DTGgSiRqPA+fcg+ G+KPtYG+ SR+G+va+asSldq G++a
  lcl|NCBI__GCF_000009985.1:WP_043743836.1 154 LVPGGSSGGSAAAVAARMVLGATGTDTGGSIRQPAAFCGITGIKPTYGRCSRFGIVAFASSLDQAGPMA 222
                                               8******************************************************************** PP

                                 TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllek 273
                                               ++v d a++l +++g+D kDsts++++v+++ ++l+ d++glkvg+ ke++ ++l++ev++ +++ +e 
  lcl|NCBI__GCF_000009985.1:WP_043743836.1 223 RTVRDCAIMLGAMAGHDPKDSTSVNMAVPDFERALTGDIRGLKVGIPKEYRPDGLSDEVAKVWDRGIEW 291
                                               ********************************************************************* PP

                                 TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342
                                               l++ ga+ ve+slp+ k+ala+Yyii+p+E ssnlarydg+ryG rv  ++ l+++y+k+R++gfg+ev
  lcl|NCBI__GCF_000009985.1:WP_043743836.1 292 LKAAGATPVEISLPHTKYALATYYIIAPAECSSNLARYDGLRYGLRVPGKT-LDDMYKKSRAAGFGAEV 359
                                               ***********************************************9999.***************** PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyls 411
                                               +rRi++G+y+ls++yyd+yy+kAqkvr+li+++f+k+fe vDvi++ptap  af +ge ++dp++m+l+
  lcl|NCBI__GCF_000009985.1:WP_043743836.1 360 RRRILIGTYVLSAGYYDAYYAKAQKVRRLIAEDFRKAFETVDVILTPTAPSAAFGMGEGTDDPVTMWLN 428
                                               ********************************************************************* PP

                                 TIGR00132 412 DvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               Dv+t+p ++aGlp++s+P+g + +glp+Glq+ig+ fd++++++va  +e a
  lcl|NCBI__GCF_000009985.1:WP_043743836.1 429 DVFTIPTSMAGLPGLSLPAGLSADGLPLGLQLIGRPFDEETVFRVAGVMETA 480
                                               *********************************************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (490 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: 7.82
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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