Alignments for a candidate for trpD_2 in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Shewanella amazonensis SB2B

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 6937998 Sama_2131 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__SB2B:6937998
          Length = 344

 Score =  253 bits (647), Expect = 4e-72
 Identities = 147/315 (46%), Positives = 194/315 (61%), Gaps = 7/315 (2%)

Query: 10  GEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAAR--PLR 67
           G  L  EEA  +  +L+ GE+  V  A LL+AL +RGE   EI+  A AMREAA   P  
Sbjct: 15  GNPLSREEAKCLFASLVRGELDEVTIAALLMALKVRGETIDEISGAADAMREAANSFPRP 74

Query: 68  VHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGV 127
                +LDIVGTGGDG   +N+ST A  VAAA G  VAKHGNR+ SS++GS+DLL   G+
Sbjct: 75  ALDGGILDIVGTGGDGFNTINISTTATFVAAAAGANVAKHGNRSVSSKSGSSDLLGQFGI 134

Query: 128 DLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADA 187
           +L   P+     +E LG  FLFA  +H  ++H  PVR +L  RT+FN+LGPL NP+  D 
Sbjct: 135 ELTMAPQTAANCLEALGICFLFAPHYHGGVKHAVPVRQKLATRTLFNVLGPLINPSHPDF 194

Query: 188 YVLGVFSPEWLAPMAEALERLGA-RGLVVHGEGADELVL-GENRVVEVGKGA---YALTP 242
            +LGV+S   + P+AE L  LG  R +VVHGEG DE+ L G  +V E+  G    Y+L+P
Sbjct: 195 MLLGVYSETLVRPIAEVLCALGVKRAMVVHGEGLDEVALHGTTQVCELRNGELVDYSLSP 254

Query: 243 EEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKE 302
           ++ GL+   +  L+GG PE+NA +   +LKGE K    DAVAL AG   Y AG   + + 
Sbjct: 255 KDFGLEPVQVTELEGGSPEDNALITAAILKGEGKAAHRDAVALNAGCALYVAGLADTPQA 314

Query: 303 GVALAREVLASGEAY 317
           G  LA + LASG+AY
Sbjct: 315 GFKLAIDTLASGKAY 329


Lambda     K      H
   0.317    0.136    0.380 

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: 299
Number of extensions: 14
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: 329
Length of database: 344
Length adjustment: 28
Effective length of query: 301
Effective length of database: 316
Effective search space:    95116
Effective search space used:    95116
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 6937998 Sama_2131 (anthranilate phosphoribosyltransferase (RefSeq))
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# 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/TIGR01245.hmm
# target sequence database:        /tmp/gapView.1088.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
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-128  415.1   0.0   1.3e-128  414.9   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937998  Sama_2131 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937998  Sama_2131 anthranilate phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   0.0  1.3e-128  1.3e-128       2     326 ..      10     334 ..       9     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 1.3e-128
                         TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke.eseelvDivGT 77 
                                        k + ++ Ls+eea+ l+  +++ge++++ iaA+l+al+v+get++ei+g+a a+re a+ +++   +  ++DivGT
  lcl|FitnessBrowser__SB2B:6937998  10 DKTYGGNPLSREEAKCLFASLVRGELDEVTIAALLMALKVRGETIDEISGAADAMREAANSFPRPaLDGGILDIVGT 86 
                                       56788999******************************************************99756778******* PP

                         TIGR01245  78 GGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpa 154
                                       GGDg++tiNiST++ +vaaaaG++vaKhGnrsvssksGs+D+L ++g++l + p+ +a++le +gi+FlfAP+yh +
  lcl|FitnessBrowser__SB2B:6937998  87 GGDGFNTINISTTATFVAAAAGANVAKHGNRSVSSKSGSSDLLGQFGIELTMAPQTAANCLEALGICFLFAPHYHGG 163
                                       ***************************************************************************** PP

                         TIGR01245 155 lkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkv 231
                                       +k+++pvR++L++rt+fN+LGPL+nP ++++ +lGvys+ lv+ +aevl +lgvkra+vvhg +glDE++l+g+t+v
  lcl|FitnessBrowser__SB2B:6937998 164 VKHAVPVRQKLATRTLFNVLGPLINPSHPDFMLLGVYSETLVRPIAEVLCALGVKRAMVVHG-EGLDEVALHGTTQV 239
                                       **************************************************************.************** PP

                         TIGR01245 232 aelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegv 308
                                       +el++ge  +y+lsp+dfgl++ +++el+ggs+e+na ++ ++l+g++k a+rd+v+lNa+ alyvag a++ ++g+
  lcl|FitnessBrowser__SB2B:6937998 240 CELRNGELVDYSLSPKDFGLEPVQVTELEGGSPEDNALITAAILKGEGKAAHRDAVALNAGCALYVAGLADTPQAGF 316
                                       ***************************************************************************** PP

                         TIGR01245 309 elakeaiksgkaleklee 326
                                       +la +++ sgka+ekl  
  lcl|FitnessBrowser__SB2B:6937998 317 KLAIDTLASGKAYEKLIG 334
                                       **************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (344 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: 00:00:00.01
# Mc/sec: 9.02
//
[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