Alignments for a candidate for hutH in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Shewanella amazonensis SB2B

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 6937475 Sama_1631 histidine ammonia-lyase (RefSeq)

Query= reanno::SB2B:6937475
         (497 letters)



>FitnessBrowser__SB2B:6937475
          Length = 497

 Score =  975 bits (2520), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MRFRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVDVMAASDKAIYGINTGFG 60
           MRFRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVDVMAASDKAIYGINTGFG
Sbjct: 1   MRFRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVDVMAASDKAIYGINTGFG 60

Query: 61  PLCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVE 120
           PLCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVE
Sbjct: 61  PLCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVE 120

Query: 121 RMLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGL 180
           RMLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGL
Sbjct: 121 RMLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGL 180

Query: 181 EPLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAEL 240
           EPLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAEL
Sbjct: 181 EPLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAEL 240

Query: 241 HEIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKE 300
           HEIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKE
Sbjct: 241 HEIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKE 300

Query: 301 LAEIEMNSVTDNPIVISAEEAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEG 360
           LAEIEMNSVTDNPIVISAEEAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEG
Sbjct: 301 LAEIEMNSVTDNPIVISAEEAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEG 360

Query: 361 LHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSIS 420
           LHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSIS
Sbjct: 361 LHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSIS 420

Query: 421 GRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKP 480
           GRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKP
Sbjct: 421 GRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKP 480

Query: 481 DIDAIIALVKAQAFTVK 497
           DIDAIIALVKAQAFTVK
Sbjct: 481 DIDAIIALVKAQAFTVK 497


Lambda     K      H
   0.319    0.136    0.387 

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: 934
Number of extensions: 21
Number of successful extensions: 1
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 6937475 Sama_1631 (histidine ammonia-lyase (RefSeq))
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# 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.carbon/TIGR01225.hmm
# target sequence database:        /tmp/gapView.6383.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.5e-183  596.1   0.2     3e-183  595.8   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6937475  Sama_1631 histidine ammonia-lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937475  Sama_1631 histidine ammonia-lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.8   0.2    3e-183    3e-183       6     495 ..       8     495 ..       5     497 .] 0.99

  Alignments for each domain:
  == domain 1  score: 595.8 bits;  conditional E-value: 3e-183
                         TIGR01225   6 esltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedlaeLqrnlvrsHa 82 
                                       ++ltle ++ +a  + ++el ++a +++++sr+ ++ ++a+dk++YG+ntGFG l +++i  ++++ Lq+nl+  Ha
  lcl|FitnessBrowser__SB2B:6937475   8 DHLTLETVNGIANGSIQAELCQQAIDKINASRHNVDVMAASDKAIYGINTGFGPLCDTQISPAETHLLQKNLLITHA 84 
                                       679************************************************************************** PP

                         TIGR01225  83 aGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalvliGeGe 159
                                       +GvGep+ +++++++l++++++l++G+sg+r +v+e ++a++  + +Pvvpe+GsvGasGDLAPL+hl l l+GeGe
  lcl|FitnessBrowser__SB2B:6937475  85 VGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVERMLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGE 161
                                       ***************************************************************************** PP

                         TIGR01225 160 aefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallgtskafdp 236
                                        +   ++++a eaL+a+gleP++l+akEGlALinGtq++ + a++al++   ll  ad+a+a+s+e+++g++++f +
  lcl|FitnessBrowser__SB2B:6937475 162 FWQGDKIVPAREALKAHGLEPLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRA 238
                                       ***************************************************************************** PP

                         TIGR01225 237 dihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiElnsatDnPlv 313
                                       ++he+rp  g+i+vaar+r++ ++se + sh+d+drvqD+YslRciPqvhGa +++ +++ke ++iE+ns+tDnP+v
  lcl|FitnessBrowser__SB2B:6937475 239 ELHEIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKELAEIEMNSVTDNPIV 315
                                       ***************************************************************************** PP

                         TIGR01225 314 fadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvs 390
                                       +++e e +sgG FHg+p+A++ld+  ia+aelg+is+RR  +ll+  l +Lp  L+  +GlnsG+mi+qy +AaLv 
  lcl|FitnessBrowser__SB2B:6937475 316 ISAE-EAISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLE-GLHGLPRLLTTSGGLNSGMMIPQYVTAALVT 390
                                       ***7.9**********************************99997.689**************************** PP

                         TIGR01225 391 enkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRe 467
                                       enk+L+ P s+Ds+pts  qEDHvsmg +++rkl ++  n++++ aiEl+ aaq+++fr++++ +  +e+  +++Re
  lcl|FitnessBrowser__SB2B:6937475 391 ENKSLCFPPSADSVPTSMGQEDHVSMGSISGRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIRE 467
                                       ***************************************************************************** PP

                         TIGR01225 468 vveeleeDRvlapDleavkellekesle 495
                                       +v++leeDR l+pD++a+  l++++ ++
  lcl|FitnessBrowser__SB2B:6937475 468 KVAKLEEDRLLKPDIDAIIALVKAQAFT 495
                                       **********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (497 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.82
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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 catabolism of small carbon sources