Alignments for a candidate for gatB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pedobacter sp. GW460-11-11-14-LB5

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate CA265_RS09170 CA265_RS09170 glutaminyl-tRNA synthase (glutamine-hydrolyzing) subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Pedo557:CA265_RS09170
          Length = 487

 Score =  398 bits (1023), Expect = e-115
 Identities = 209/475 (44%), Positives = 299/475 (62%), Gaps = 5/475 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           FE V GLE+HV+L T++K+FS   A FGA PN N + + LA PG LP +NK  V  A+R 
Sbjct: 12  FELVSGLEIHVQLNTNTKIFSADSASFGALPNQNISTVSLALPGALPKLNKEVVAKAIRI 71

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            +ALN  I   + FDRKNYFY D PK YQI+Q +QPI  NG++++++ DG TK+IGI R+
Sbjct: 72  GLALNCTINQTNHFDRKNYFYADLPKGYQITQDNQPICVNGFLELQLADGSTKKIGINRI 131

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+EEDAGKS H  +  YSLVDLNR G PLIEIV+EPDIRS +EA   L ++R ++++  V
Sbjct: 132 HLEEDAGKSIHDQDDNYSLVDLNRAGVPLIEIVTEPDIRSSEEASVLLSEIRKLVRHLNV 191

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
           SD  MEEGSLRCDANIS+RP G  +FGT+ E+KNLNS   VR+ +++E  RQ E +  GG
Sbjct: 192 SDGNMEEGSLRCDANISIRPQGSTEFGTRCEVKNLNSMRNVRRAMDFEFGRQVEVISEGG 251

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
           +I Q T  FD   G T  MR KE ++DYRYF +PD+ P++I DAW   ++  +P LP+E 
Sbjct: 252 KIIQSTLNFDADKGTTSPMRTKEEANDYRYFSDPDLQPIHISDAWLAEIKSLMPALPNEI 311

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359
             + V+E G+   DA +     ++ ++F        + K   NWL+G +   LN+  + +
Sbjct: 312 SKQMVSEFGISKADATLFAEDLDLLNYFNQAQSAVHNKKSLINWLIGPIRAVLNEKGMAI 371

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAK--QIMEDNGLVQISDEAT 417
            D K+ P  LA  I L++D  ++ +IA +          NAK   + +   L+   +   
Sbjct: 372 TDFKVNPAQLAEAINLVDDKKITQQIAIQQLLPAVELEANAKVTDLAQSLNLLISENGDE 431

Query: 418 LLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           L  F++E L+   Q VE YK GK   +G  VG +MK +KG+A+ + +N+L+ ++L
Sbjct: 432 LSSFIDEVLNKYPQQVEAYKKGKKGVLGLFVGDVMKLAKGKADAKKLNELILEKL 486


Lambda     K      H
   0.313    0.133    0.373 

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: 615
Number of extensions: 23
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: 475
Length of database: 487
Length adjustment: 34
Effective length of query: 441
Effective length of database: 453
Effective search space:   199773
Effective search space used:   199773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS09170 CA265_RS09170 (glutaminyl-tRNA synthase (glutamine-hydrolyzing) subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.12763.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-167  544.2   1.1   1.3e-167  544.0   1.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09170  CA265_RS09170 glutaminyl-tRNA sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09170  CA265_RS09170 glutaminyl-tRNA synthase (glutamine-hydrolyzing) subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.0   1.1  1.3e-167  1.3e-167       2     480 ..      10     486 ..       9     487 .] 0.97

  Alignments for each domain:
  == domain 1  score: 544.0 bits;  conditional E-value: 1.3e-167
                                  TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                                + +elv GlE+Hvqlnt++K+F+  s ++    pN+n++ v l+lPGalP lNke+v+kA+ ++laln
  lcl|FitnessBrowser__Pedo557:CA265_RS09170  10 TPFELVSGLEIHVQLNTNTKIFSADSASFGA-LPNQNISTVSLALPGALPKLNKEVVAKAIRIGLALN 76 
                                                5799*************************99.9*********************************** PP

                                  TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqyk 136
                                                + i+ ++  FdRK+YfY DlPkgyqitq ++Pi+ +G le++l +++ k+igi+r+hlEeD+gks + 
  lcl|FitnessBrowser__Pedo557:CA265_RS09170  77 CTIN-QTNHFDRKNYFYADLPKGYQITQDNQPICVNGFLELQLADGStKKIGINRIHLEEDAGKSIHD 143
                                                **66.69***********************************987666******************** PP

                                  TIGR00133 137 esdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsi 204
                                                ++d  ++slvD+NR+gvPL+EiVt+Pd++s++ea   l+++r+++r+l++sdg++eeGs+R+D+N+si
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 144 QDD--NYSLVDLNRAGVPLIEIVTEPDIRSSEEASVLLSEIRKLVRHLNVSDGNMEEGSLRCDANISI 209
                                                886..8************************************************************** PP

                                  TIGR00133 205 rlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeese 272
                                                r++G++++gtr E+KNlns++++ +a+++E  Rq++++++g ++ q t +fd  k +t  +R Kee++
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 210 RPQGSTEFGTRCEVKNLNSMRNVRRAMDFEFGRQVEVISEGGKIIQSTLNFDADKGTTSPMRTKEEAN 277
                                                ******************************************************************** PP

                                  TIGR00133 273 DYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvk 340
                                                DYRYf +Pdl+pi+i++ ++ e ++  +p lP++  +++++e+g+s+ da +  +dl+ll++f+++++
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 278 DYRYFSDPDLQPIHISDAWLAE-IKSLMPALPNEISKQMVSEFGISKADATLFAEDLDLLNYFNQAQS 344
                                                ********************99.9******************************************** PP

                                  TIGR00133 341 likepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksake.lleel.lenkk 406
                                                +++++k  +nW++  ++++Ln+k + ++++ ++p +lae i+l++++ki+q++a + ll  + le + 
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 345 AVHNKKSLINWLIGPIRAVLNEKGMAITDFKVNPAQLAEAINLVDDKKITQQIAIQqLLPAVeLEANA 412
                                                ****************************************************9965166554366699 PP

                                  TIGR00133 407 dpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevek 474
                                                ++  l++ l+l   ++ +el ++++ev+++ p++ve yk+gk+ +l+++vG vmk +kg+ad+k+ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 413 KVTDLAQSLNLLISENGDELSSFIDEVLNKYPQQVEAYKKGKKGVLGLFVGDVMKLAKGKADAKKLNE 480
                                                9******************************************************************* PP

                                  TIGR00133 475 llkell 480
                                                l+ e+l
  lcl|FitnessBrowser__Pedo557:CA265_RS09170 481 LILEKL 486
                                                ***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (487 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: 00:00:00.03
# Mc/sec: 7.48
//
[ok]

This GapMind analysis is from Apr 09 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