Alignments for a candidate for argD'B in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD'B in Shewanella amazonensis SB2B

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__SB2B:6937472
          Length = 405

 Score =  534 bits (1375), Expect = e-156
 Identities = 261/402 (64%), Positives = 314/402 (78%)

Query: 5   ITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKAL 64
           I RS FDE M+P YAP+  IPV+G GSRLWDQQG+E+IDFAGGIAVN LGH HP LV AL
Sbjct: 3   INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSAL 62

Query: 65  TEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRF 124
           TEQA K WH  N  TNEP L LAK L+D TFA++V+F NSGAEANEAALKL R+ A ++F
Sbjct: 63  TEQAQKLWHLSNTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKF 122

Query: 125 GSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNT 184
           G++KS I+AFK  FHGRTLFTVS GGQPAYS  F P P  I HA YN+LDS KALI D T
Sbjct: 123 GADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRT 182

Query: 185 CAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVT 244
           CAV++EP+QGEGG++    +F++G+RELCD HNALL+FDEVQTGVGRTGELYAYM  GVT
Sbjct: 183 CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVT 242

Query: 245 PDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREV 304
           PD+L+TAKALGGGFPIGA+L +   A  + VGTHG+TYGGNPLACAV    F T+NT EV
Sbjct: 243 PDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEV 302

Query: 305 LNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLM 364
           LNGVK+R Q F + LNAIN +Y +F E+RG GLL+G  L  +YAGKA+     AAEEG++
Sbjct: 303 LNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVL 362

Query: 365 ILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406
           +L+AG NVVRFAP+LII E +V  GL RF+ A  + +A +++
Sbjct: 363 LLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLVARLNA 404


Lambda     K      H
   0.321    0.137    0.412 

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: 522
Number of extensions: 17
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 6937472 Sama_1628 (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.aa/TIGR03246.hmm
# target sequence database:        /tmp/gapView.9940.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-216  704.3   0.2   2.6e-216  704.1   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6937472  Sama_1628 bifunctional N-succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937472  Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine t
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.1   0.2  2.6e-216  2.6e-216       1     397 []       3     399 ..       3     399 .. 1.00

  Alignments for each domain:
  == domain 1  score: 704.1 bits;  conditional E-value: 2.6e-216
                         TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytne 77 
                                       ++r+ fdevmvp+yap+++ipv+g Gsr+wdq+g+e+idfaGGiavn+lGh+hp+lv+al+eqa+klwhl+n++tne
  lcl|FitnessBrowser__SB2B:6937472   3 INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLSNTMTNE 79 
                                       78*************************************************************************** PP

                         TIGR03246  78 pvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedf 154
                                       p+l lak+lvd+tfa+kv+f+nsGaeaneaalkl r+val+k+ga+ks+i+afk++fhGrtlftvsvGGq++ys++f
  lcl|FitnessBrowser__SB2B:6937472  80 PALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGF 156
                                       ***************************************************************************** PP

                         TIGR03246 155 aplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGel 231
                                       +p+p++i+ha+yn+l++lkalisd+tcav++ep+qGegG+++++++f+kg+relcd+hnall+fdevqtGvGrtGel
  lcl|FitnessBrowser__SB2B:6937472 157 GPKPADIDHAEYNNLDSLKALISDRTCAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGEL 233
                                       ***************************************************************************** PP

                         TIGR03246 232 yaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrh 308
                                       yaym +Gvtpd+lt+akalGgGfpiGa+ltt+elak+l vGthG+tyGGnplacav  + + +vnt+e+l+Gvk+r+
  lcl|FitnessBrowser__SB2B:6937472 234 YAYMGLGVTPDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEVLNGVKERE 310
                                       ***************************************************************************** PP

                         TIGR03246 309 elfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeG 385
                                       +lf d l++in++y+vf+e+rGkGll+Ga+l+++yaGka+d++ aaaeeGvl+l+aG +vvrfapsl+i+e+++ eG
  lcl|FitnessBrowser__SB2B:6937472 311 QLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVLLLMAGQNVVRFAPSLIIPEADVREG 387
                                       ***************************************************************************** PP

                         TIGR03246 386 larlekaveklv 397
                                       lar++ a++klv
  lcl|FitnessBrowser__SB2B:6937472 388 LARFDAAIAKLV 399
                                       ********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: 00:00:00.01
# Mc/sec: 12.22
//
[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