Alignments for a candidate for gatA in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Sphingomonas wittichii RW1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011951446.1 SWIT_RS03045 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000016765.1:WP_011951446.1
          Length = 495

 Score =  429 bits (1104), Expect = e-125
 Identities = 230/453 (50%), Positives = 304/453 (67%), Gaps = 10/453 (2%)

Query: 40  VQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENF 99
           + AF+    + A A A+  D A     E   L G+P+G+KD   T G +TT +S +L  F
Sbjct: 40  LNAFIIETPDHATAAAEAADRA-RAAGELLPLSGVPLGIKDLFCTAGHQTTAASHMLGGF 98

Query: 100 DPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPW------NLDTVPGG 153
            P Y++TV  +L  A A  +GKLN+D+FAMGSS E SAY    +PW      N    PGG
Sbjct: 99  TPTYESTVTGKLFAAGAGMLGKLNLDQFAMGSSNETSAYGNVVSPWRRNDGGNAPLAPGG 158

Query: 154 SSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQI 213
           SSGGS++A+AA  VP + G+DTGGSIRQPA+F G+ G+KPTYGR SR+G+VAFASSLDQ 
Sbjct: 159 SSGGSSSAIAARIVPAATGTDTGGSIRQPAAFTGIAGIKPTYGRCSRFGIVAFASSLDQA 218

Query: 214 GPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVG 273
           G + + V D+A LL+A+SG D  DSTS +V VP + ++L+ D+KG K+ +PKEY  + + 
Sbjct: 219 GAMAQDVRDSAILLEAMSGFDPKDSTSLDVAVPKWEANLSSDLKGKKVGIPKEYRVDNMP 278

Query: 274 KEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYR- 332
            E        ++ L   GA   +VSLPH++YAL TYY+++ +EAS+NLAR+DG+RYG R 
Sbjct: 279 AEIDALWRQGIEWLRDAGAEIVDVSLPHTRYALPTYYIIAPAEASSNLARYDGVRYGLRD 338

Query: 333 TDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDV 392
                NL ++Y  TRA GFG EVKRRI++GT+ LS+GYYDAYY KAQKVR LI +DFE+ 
Sbjct: 339 LPEGANLQEMYAATRAAGFGPEVKRRILIGTYVLSAGYYDAYYTKAQKVRALIARDFEEA 398

Query: 393 FEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPL 451
           F + DV++ PT P+ AF +GE + DPL MY ND+ T+P +LAGVP +SVP GL   GLPL
Sbjct: 399 FRQVDVLLTPTAPSAAFALGEKSADPLEMYLNDVFTVPASLAGVPAMSVPAGLDGQGLPL 458

Query: 452 GLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484
           GLQIIG+  DE  V     A EQ      AKP+
Sbjct: 459 GLQIIGRPLDEQGVLNAGLAIEQRAG-FTAKPQ 490


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: 616
Number of extensions: 27
Number of successful extensions: 4
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: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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_011951446.1 SWIT_RS03045 (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.22915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-169  548.6   0.0   6.8e-169  548.4   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_011951446.1  SWIT_RS03045 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_011951446.1  SWIT_RS03045 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 !  548.4   0.0  6.8e-169  6.8e-169      10     463 ..      21     482 ..      12     485 .. 0.95

  Alignments for each domain:
  == domain 1  score: 548.4 bits;  conditional E-value: 6.8e-169
                                 TIGR00132  10 vsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiet 76 
                                               +s++e++++++ ++   k  +naf+  t+++a+++a++ d++ a  e  +l g+p+++Kd +++ + +t
  lcl|NCBI__GCF_000016765.1:WP_011951446.1  21 FSAREIADAFNGAVAGAKA-LNAFIIETPDHATAAAEAADRARAaGElLPLSGVPLGIKDLFCTAGHQT 88 
                                               6677888888888887777.********************988876646******************** PP

                                 TIGR00132  77 tcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe......neervpG 139
                                               t+aS++L +++++y++tV+ +l +aga ++Gk NlD FamGss etSa+g +  P+      n    pG
  lcl|NCBI__GCF_000016765.1:WP_011951446.1  89 TAASHMLGGFTPTYESTVTGKLFAAGAGMLGKLNLDQFAMGSSNETSAYGNVVSPWrrndggNAPLAPG 157
                                               *******************************************************722222244579** PP

                                 TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                               GSsgGs+ a+aa +vp a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va+asSldq G +a++v 
  lcl|NCBI__GCF_000016765.1:WP_011951446.1 158 GSSGGSSSAIAARIVPAATGTDTGGSIRQPAAFTGIAGIKPTYGRCSRFGIVAFASSLDQAGAMAQDVR 226
                                               ********************************************************************* PP

                                 TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleel 277
                                               d a++l+++sg D kDstsl+v+v+++  +l +dlkg kvg+ ke++ ++++ e+++ +++ +e l++ 
  lcl|NCBI__GCF_000016765.1:WP_011951446.1 227 DSAILLEAMSGFDPKDSTSLDVAVPKWEANLSSDLKGKKVGIPKEYRVDNMPAEIDALWRQGIEWLRDA 295
                                               ********************************************************************* PP

                                 TIGR00132 278 gaeivevslpsvklalaiYyiispsEassnlarydgiryGkrv.eelkslkelyaktRsegfgeevkrR 345
                                               gaeiv+vslp+ ++al++Yyii+p+Eassnlarydg+ryG r   e  +l+e+ya+tR++gfg evkrR
  lcl|NCBI__GCF_000016765.1:WP_011951446.1 296 GAEIVDVSLPHTRYALPTYYIIAPAEASSNLARYDGVRYGLRDlPEGANLQEMYAATRAAGFGPEVKRR 364
                                               *****************************************97257778******************** PP

                                 TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414
                                               i++G+y+ls++yyd+yy+kAqkvr li+++fe++f++vDv+++ptap  af lgek +dplemyl+Dv+
  lcl|NCBI__GCF_000016765.1:WP_011951446.1 365 ILIGTYVLSAGYYDAYYTKAQKVRALIARDFEEAFRQVDVLLTPTAPSAAFALGEKSADPLEMYLNDVF 433
                                               ********************************************************************* PP

                                 TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               tvpa+laG+pa+svP+g + +glp+Glqiig+ +d++ +l+++ a+eq+
  lcl|NCBI__GCF_000016765.1:WP_011951446.1 434 TVPASLAGVPAMSVPAGLDGQGLPLGLQIIGRPLDEQGVLNAGLAIEQR 482
                                               *********************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (495 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: 8.36
//
[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