Alignments for a candidate for astC in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Shewanella loihica PV-4

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  546 bits (1407), Expect = e-160
 Identities = 267/403 (66%), Positives = 323/403 (80%), Gaps = 1/403 (0%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSV H  + RA FD+VMVPNYAP+A IPVRG GSRVWDQ G E +DFAGGIAVN LGH H
Sbjct: 1   MSVNHK-LTRAQFDEVMVPNYAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCH 59

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV AL EQ  K+WH++NV TNEPAL LA KLV+ATFAE+V+F NSGAEANEAA KLAR
Sbjct: 60  PALVGALKEQGEKIWHLANVMTNEPALALATKLVEATFAEKVYFANSGAEANEAALKLAR 119

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R A D+FG EK +I+A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+P+ND+AAL+
Sbjct: 120 RYALDKFGAEKDQIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALE 179

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           A VSDKTCA++LEP+QGEGG++ A+  +L+  R L D HNAL++FDEVQTG+GR G+L+A
Sbjct: 180 AEVSDKTCAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYA 239

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y    VTPDILT+AK+LGGGFPIAAMLTT ++A HL +GTHG+TYGGNPLACA+  AV+D
Sbjct: 240 YMRTEVTPDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLD 299

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVL+GV  +    +  L QI EKY +FTEVRG GLLLG VL++ ++G++KD   A
Sbjct: 300 VVNTPEVLDGVKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVA 359

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
              EGLM L AGP+VIRF PSLV+ +ADI  GL RFERA AK+
Sbjct: 360 GTSEGLMCLIAGPNVIRFTPSLVIPEADIAEGLARFERAVAKV 402


Lambda     K      H
   0.320    0.136    0.400 

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: 503
Number of extensions: 10
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: 406
Length of database: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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: 50 (23.9 bits)

Align candidate 5208066 Shew_0578 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.18289.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.9e-215  701.2   0.4   2.2e-215  701.0   0.4    1.0  1  lcl|FitnessBrowser__PV4:5208066  Shew_0578 bifunctional N-succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208066  Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine tr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.0   0.4  2.2e-215  2.2e-215       2     397 .]       8     403 ..       7     403 .. 1.00

  Alignments for each domain:
  == domain 1  score: 701.0 bits;  conditional E-value: 2.2e-215
                        TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepv 79 
                                      +r++fdevmvp+yap+++ipvrgeGsrvwdqeg+e++dfaGGiavn+lGh+hp+lv alkeq+ek+whl+n++tnep+
  lcl|FitnessBrowser__PV4:5208066   8 TRAQFDEVMVPNYAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLANVMTNEPA 85 
                                      89**************************************************************************** PP

                        TIGR03246  80 lrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfapl 157
                                      l+la klv+atfa+kv+f+nsGaeaneaalklar++aldk+gaek++i+af ++fhGrt+ftvsvGGqa+ys++f+p+
  lcl|FitnessBrowser__PV4:5208066  86 LALATKLVEATFAEKVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPK 163
                                      ****************************************************************************** PP

                        TIGR03246 158 pegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaym 235
                                      p+ i+h+++nd++al+a +sdktca+++ep+qGegG++ ad++fl+++r+l d+hnal+ifdevqtGvGr+Gelyaym
  lcl|FitnessBrowser__PV4:5208066 164 PQSITHLPFNDIAALEAEVSDKTCAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYM 241
                                      ****************************************************************************** PP

                        TIGR03246 236 eyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvd 313
                                       + vtpdilt+akalGgGfpi a+ltt+e+a++lk+GthG+tyGGnplaca+ ++vld+vnt+e+l+Gvk+r++l+ d
  lcl|FitnessBrowser__PV4:5208066 242 RTEVTPDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLDGVKRREQLLRD 319
                                      ****************************************************************************** PP

                        TIGR03246 314 elekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlek 391
                                       l++in++y+vf+e+rG+Gll+Gavl+e+y+G++kd++ a ++eG++ liaGp+v+rf+pslvi+e++i+eGlar+e+
  lcl|FitnessBrowser__PV4:5208066 320 GLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVAGTSEGLMCLIAGPNVIRFTPSLVIPEADIAEGLARFER 397
                                      ****************************************************************************** PP

                        TIGR03246 392 aveklv 397
                                      av+k+v
  lcl|FitnessBrowser__PV4:5208066 398 AVAKVV 403
                                      **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (405 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 6.98
//
[ok]

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

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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

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