Alignments for a candidate for gatA in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Sinorhizobium medicae WSM419

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate YP_001326634.1 Smed_0944 aspartyl/glutamyl-tRNA amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000017145.1:YP_001326634.1
          Length = 493

 Score =  472 bits (1214), Expect = e-137
 Identities = 250/477 (52%), Positives = 330/477 (69%), Gaps = 11/477 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I E +  +  KEI   +L D     I+A ++ + A++A+  ++AR  AK  D  + G  +
Sbjct: 9   IAEARAKLSDKEITAVELTDAYLAAIEAANETINAYIAVTPDKAREMAKASDARI-GAGK 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+P+G+KD   T+GL T   S IL+ F P Y++TV Q L +  AV +GKLNMDEF
Sbjct: 68  AGALEGIPLGIKDLFGTQGLHTQACSHILDGFRPHYESTVTQNLWNDGAVMLGKLNMDEF 127

Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           AMGSS E S Y   KNPW     NLD VPGGSSGGSAAAVAA     +  +DTGGSIRQP
Sbjct: 128 AMGSSNETSYYGPVKNPWRAKESNLDLVPGGSSGGSAAAVAARLCAGATATDTGGSIRQP 187

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           A+F G VG+KPTYGR SR+G++AFASSLDQ GPI R V D A LL++++ VD  D+TS +
Sbjct: 188 AAFTGTVGIKPTYGRCSRWGVIAFASSLDQAGPIARDVRDAAILLKSMASVDPKDTTSVD 247

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
           + VPD+ +++   IKG++I +PKEY  EG+ +E        +  L+  GA   ++SLPH+
Sbjct: 248 LPVPDYEAAIGQSIKGMRIGIPKEYRVEGMPEEIEALWQQGVAWLKDAGAEIVDISLPHT 307

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           KYAL  YY+++ +EAS+NLAR+DG+RYG R D  D ++D+Y++TRA GFG EVKRRIM+G
Sbjct: 308 KYALPAYYIVAPAEASSNLARYDGVRYGLRVDGKD-IVDMYEKTRAAGFGQEVKRRIMIG 366

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGEN--TKDPL 419
           T+ LS+GYYDAYY +AQKVRTLIK+DFE  F    D I+ P TP+ AF I +     DP+
Sbjct: 367 TYVLSAGYYDAYYLRAQKVRTLIKRDFELAFHAGVDAILTPATPSSAFGIADEDLASDPV 426

Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
            MY NDI T+ VN+AG+PGI+VP GL   GLPLGLQ+IGK FDE T+++ AH  EQA
Sbjct: 427 KMYLNDIFTVTVNMAGLPGIAVPGGLDHKGLPLGLQLIGKPFDEETLFKTAHVIEQA 483


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: 627
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: 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 YP_001326634.1 Smed_0944 (aspartyl/glutamyl-tRNA amidotransferase 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.26007.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-176  572.2   0.0   4.7e-176  572.0   0.0    1.0  1  lcl|NCBI__GCF_000017145.1:YP_001326634.1  Smed_0944 aspartyl/glutamyl-tRNA


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001326634.1  Smed_0944 aspartyl/glutamyl-tRNA amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.0   0.0  4.7e-176  4.7e-176       3     463 ..      14     483 ..      12     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 572.0 bits;  conditional E-value: 4.7e-176
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               ++l +ke++++e+++++l++iea +++ina+++vt++ka ++ak++d+++   +   l gip+++Kd +
  lcl|NCBI__GCF_000017145.1:YP_001326634.1  14 AKLSDKEITAVELTDAYLAAIEAANETINAYIAVTPDKAREMAKASDARIGaGKaGALEGIPLGIKDLF 82 
                                               67899*********************************************874436************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....en 133
                                                +++++t + S+iL+++++ y++tV+++l ++ga+++Gk N+DEFamGss etS++g++knP      n
  lcl|NCBI__GCF_000017145.1:YP_001326634.1  83 GTQGLHTQACSHILDGFRPHYESTVTQNLWNDGAVMLGKLNMDEFAMGSSNETSYYGPVKNPwrakeSN 151
                                               **************************************************************5555557 PP

                                 TIGR00132 134 eervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGi 202
                                                + vpGGSsgGsaaavaa l+  a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G++a+asSldq G+
  lcl|NCBI__GCF_000017145.1:YP_001326634.1 152 LDLVPGGSSGGSAAAVAARLCAGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGVIAFASSLDQAGP 220
                                               789****************************************************************** PP

                                 TIGR00132 203 lakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekll 271
                                               +a++v d+a++l+ ++ +D kD+ts++ +v+++  ++ + +kg+++g+ ke++ e++++e+++ +++ +
  lcl|NCBI__GCF_000017145.1:YP_001326634.1 221 IARDVRDAAILLKSMASVDPKDTTSVDLPVPDYEAAIGQSIKGMRIGIPKEYRVEGMPEEIEALWQQGV 289
                                               ********************************************************************* PP

                                 TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                                 l++ gaeiv++slp+ k+al++Yyi++p+Eassnlarydg+ryG rv+ ++ + ++y ktR++gfg+
  lcl|NCBI__GCF_000017145.1:YP_001326634.1 290 AWLKDAGAEIVDISLPHTKYALPAYYIVAPAEASSNLARYDGVRYGLRVDGKD-IVDMYEKTRAAGFGQ 357
                                               *************************************************9888.*************** PP

                                 TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfe.evDvivsptaptlafklgek..aedpl 406
                                               evkrRim+G+y+ls++yyd+yy++Aqkvrtli+++fe +f+  vD i++p++p +af ++++  a+dp+
  lcl|NCBI__GCF_000017145.1:YP_001326634.1 358 EVKRRIMIGTYVLSAGYYDAYYLRAQKVRTLIKRDFELAFHaGVDAILTPATPSSAFGIADEdlASDPV 426
                                               **************************************99637****************87633678** PP

                                 TIGR00132 407 emylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               +myl+D++tv++n+aGlp+i+vP g ++kglp+Glq+igk fd+++l++ a+ +eqa
  lcl|NCBI__GCF_000017145.1:YP_001326634.1 427 KMYLNDIFTVTVNMAGLPGIAVPGGLDHKGLPLGLQLIGKPFDEETLFKTAHVIEQA 483
                                               ******************************************************997 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.91
//
[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