Alignments for a candidate for gatA in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Rhodobacter sphaeroides ATCC 17029

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011840706.1 RSPH17029_RS04815 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000015985.1:WP_011840706.1
          Length = 491

 Score =  451 bits (1160), Expect = e-131
 Identities = 242/476 (50%), Positives = 325/476 (68%), Gaps = 11/476 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I E +  + + E+   DL       I A    + AF+    E A   A+  D      + 
Sbjct: 8   IAEARDALARGELSAVDLTMACLTAIDA-GTPLNAFVHTTPEIALDQARAADARRGAGA- 65

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+P+G+KD   T+G+ +  +S IL  F P Y++TV  +L +A AV +GKLNMDEF
Sbjct: 66  -GALNGIPLGIKDLFCTRGVASQAASNILRGFKPEYESTVTSKLFEAGAVMLGKLNMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDT---VPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPAS 184
           AMGSS E S Y    NPW +D     PGGSSGGSAAAVAA     + G+DTGGSIRQPA+
Sbjct: 125 AMGSSNETSCYGDAVNPWKVDDRRLTPGGSSGGSAAAVAADLCLAATGTDTGGSIRQPAA 184

Query: 185 FCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVD 244
           F G+VG+KPTYGRVSR+G+VAFASSLDQ GP+T++V D A LL A++G D  DSTSA++ 
Sbjct: 185 FTGIVGIKPTYGRVSRWGIVAFASSLDQAGPMTKSVRDAAILLGAMAGHDPKDSTSADIP 244

Query: 245 VPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           VPDF ++LTGDI+G KI +P+EY  EG+  E         ++L   GA   ++SLPH+KY
Sbjct: 245 VPDFEAALTGDIRGRKIGIPREYRMEGMPAEIEALWARGREMLADAGAEIVDISLPHTKY 304

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRT--DNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
           AL  YY+++ +EAS+NLAR+DG+RYG+R      D ++D+Y++TRAEGFG EV+RR+M+G
Sbjct: 305 ALPAYYVIAPAEASSNLARYDGVRYGHRARLGQGDGIVDMYEKTRAEGFGKEVQRRVMIG 364

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGENT-KDPLT 420
           T+ LS+G+YDAYY +A+KVR LIK+DF++ F    D I+ P TP+ AF +GE    DP+ 
Sbjct: 365 TYVLSAGFYDAYYNRARKVRALIKRDFDEAFAAGVDAILTPATPSSAFGLGEMADADPVA 424

Query: 421 MYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           MY ND+ T+ VNLAG+PGISVP GL A GLPLGLQ+IG+ +DE+ +   AH  E+A
Sbjct: 425 MYLNDVFTVTVNLAGLPGISVPVGLDAKGLPLGLQLIGRPWDEAGLLNHAHVLERA 480


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: 597
Number of extensions: 29
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_011840706.1 RSPH17029_RS04815 (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.2996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-169  548.4   0.0   7.8e-169  548.2   0.0    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011840706.1  RSPH17029_RS04815 Asp-tRNA(Asn)/


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011840706.1  RSPH17029_RS04815 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subun
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.2   0.0  7.8e-169  7.8e-169       3     463 ..      13     480 ..      11     483 .. 0.96

  Alignments for each domain:
  == domain 1  score: 548.2 bits;  conditional E-value: 7.8e-169
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.kekklagipiavKdnia 70 
                                               ++l + e+s+++++ ++l +i+a +  +naf+++t+e al +a++ d++       l+gip+++Kd ++
  lcl|NCBI__GCF_000015985.1:WP_011840706.1  13 DALARGELSAVDLTMACLTAIDAGTP-LNAFVHTTPEIALDQARAADARRGaGAGALNGIPLGIKDLFC 80 
                                               56788899999***********9999.********************98863447************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe...neer 136
                                               ++++   +aS+iL+++++ y++tV+ +l eaga+++Gk N+DEFamGss etS++g   nP+   +++ 
  lcl|NCBI__GCF_000015985.1:WP_011840706.1  81 TRGVASQAASNILRGFKPEYESTVTSKLFEAGAVMLGKLNMDEFAMGSSNETSCYGDAVNPWkvdDRRL 149
                                               *************************************************************73325667 PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                                pGGSsgGsaaavaadl+  a g+DTGgSiRqPA+f+g+vG+KPtYG+vSR+G+va+asSldq G+++k
  lcl|NCBI__GCF_000015985.1:WP_011840706.1 150 TPGGSSGGSAAAVAADLCLAATGTDTGGSIRQPAAFTGIVGIKPTYGRVSRWGIVAFASSLDQAGPMTK 218
                                               8******************************************************************** PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               +v d+a++l +++g+D kDsts++++v+++  +l+ d++g k+g+ +e++ e+++ e+++ +++  e l
  lcl|NCBI__GCF_000015985.1:WP_011840706.1 219 SVRDAAILLGAMAGHDPKDSTSADIPVPDFEAALTGDIRGRKIGIPREYRMEGMPAEIEALWARGREML 287
                                               ********************************************************************* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelks..lkelyaktRsegfgee 341
                                                + gaeiv++slp+ k+al++Yy+i+p+Eassnlarydg+ryG+r++  +   + ++y ktR+egfg+e
  lcl|NCBI__GCF_000015985.1:WP_011840706.1 288 ADAGAEIVDISLPHTKYALPAYYVIAPAEASSNLARYDGVRYGHRARLGQGdgIVDMYEKTRAEGFGKE 356
                                               ********************************************987554445**************** PP

                                 TIGR00132 342 vkrRimlGayalskeyydkyykkAqkvrtliidefeklf.eevDvivsptaptlafklgekaed.plem 408
                                               v+rR+m+G+y+ls++ yd+yy++A kvr li+++f+++f   vD i++p++p +af lge a+  p++m
  lcl|NCBI__GCF_000015985.1:WP_011840706.1 357 VQRRVMIGTYVLSAGFYDAYYNRARKVRALIKRDFDEAFaAGVDAILTPATPSSAFGLGEMADAdPVAM 425
                                               ***************************************457******************99866**** PP

                                 TIGR00132 409 ylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               yl+Dv+tv++nlaGlp+isvP+g + kglp+Glq+ig+ +d+  ll+ a+ le+a
  lcl|NCBI__GCF_000015985.1:WP_011840706.1 426 YLNDVFTVTVNLAGLPGISVPVGLDAKGLPLGLQLIGRPWDEAGLLNHAHVLERA 480
                                               ************************************************9999976 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.79
//
[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