Alignments for a candidate for astC in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Shewanella amazonensis SB2B

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

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



>FitnessBrowser__SB2B:6938908
          Length = 404

 Score =  536 bits (1381), Expect = e-157
 Identities = 258/394 (65%), Positives = 315/394 (79%)

Query: 10  RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTE 69
           RA FD+VMVPNYAPAA IPVRG GSRVWDQ G E +DFAGGIAVN LGH HPALV AL E
Sbjct: 9   RAQFDEVMVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKE 68

Query: 70  QANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGT 129
           Q  KLWH+SN  TNEPAL LA KLV+ATFA+RV+F NSGAEANEAA KLARR A ++FG 
Sbjct: 69  QGEKLWHLSNTMTNEPALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGE 128

Query: 130 EKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCA 189
            K E++A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+P+ND+AAL+AAVSD TCA
Sbjct: 129 HKVEVIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPAAITHLPFNDIAALEAAVSDNTCA 188

Query: 190 VVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPD 249
           ++LEP+QGEGG++  +  +L+  R L D HNAL++FDEVQTG+GR+G L+AY    + PD
Sbjct: 189 IMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPD 248

Query: 250 ILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLN 309
           ILT+AK+LGGGFPIAAMLTT D+A HL VGTHG+TYGGNPLACA+  AV+DV+NTPEVL+
Sbjct: 249 ILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLD 308

Query: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMIL 369
           GV  +   F+  L QI EKY +F+E+RG GLLLG VL++ + G+++D  NA+  EGL+ L
Sbjct: 309 GVKHREQLFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTL 368

Query: 370 QAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
            AG +V+RF PSLV+ +ADI  GL RFERA AK+
Sbjct: 369 MAGANVVRFTPSLVIPEADIVEGLARFERAVAKV 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: 501
Number of extensions: 8
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: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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 6938908 Sama_3011 (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.6229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.5e-212  689.8   1.5   6.2e-212  689.7   1.5    1.0  1  lcl|FitnessBrowser__SB2B:6938908  Sama_3011 bifunctional N-succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938908  Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine t
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.7   1.5  6.2e-212  6.2e-212       2     396 ..       8     402 ..       7     403 .. 1.00

  Alignments for each domain:
  == domain 1  score: 689.7 bits;  conditional E-value: 6.2e-212
                         TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnep 78 
                                       +r++fdevmvp+yapa++ipvrgeGsrvwdq+g ey+dfaGGiavn+lGh+hp+lv alkeq+eklwhl+n++tnep
  lcl|FitnessBrowser__SB2B:6938908   8 TRAQFDEVMVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWHLSNTMTNEP 84 
                                       89*************************************************************************** PP

                         TIGR03246  79 vlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfa 155
                                       +l+la klv+atfad+v+f+nsGaeaneaalklar++a++k+g++k e++af ++fhGrt+ftvsvGGqa+ys++f+
  lcl|FitnessBrowser__SB2B:6938908  85 ALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGEHKVEVIAFDKAFHGRTFFTVSVGGQAAYSDGFG 161
                                       ***************************************************************************** PP

                         TIGR03246 156 plpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGely 232
                                       p+p+ i+h+++nd++al+a++sd+tca+++ep+qGegG+++ d++fl+++r+l d+hnal+ifdevqtGvGrtG+ly
  lcl|FitnessBrowser__SB2B:6938908 162 PKPAAITHLPFNDIAALEAAVSDNTCAIMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLY 238
                                       ***************************************************************************** PP

                         TIGR03246 233 aymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhe 309
                                       aym + ++pdilt+akalGgGfpi a+ltt ++a++lkvGthG+tyGGnplaca+ ++v+d+vnt+e+l+Gvk+r++
  lcl|FitnessBrowser__SB2B:6938908 239 AYMGTEIVPDILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLDGVKHREQ 315
                                       ***************************************************************************** PP

                         TIGR03246 310 lfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGl 386
                                       lf d l++in++y+vfseirGkGll+Gavl+e++aG+++d++na+ +eG+l l+aG++vvrf+pslvi+e++i eGl
  lcl|FitnessBrowser__SB2B:6938908 316 LFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTLMAGANVVRFTPSLVIPEADIVEGL 392
                                       ***************************************************************************** PP

                         TIGR03246 387 arlekavekl 396
                                       ar+e+av+k+
  lcl|FitnessBrowser__SB2B:6938908 393 ARFERAVAKV 402
                                       *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (404 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: 9.27
//
[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