GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD 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= BRENDA::O30508
         (406 letters)



>FitnessBrowser__SB2B:6937472
          Length = 405

 Score =  526 bits (1356), Expect = e-154
 Identities = 256/397 (64%), Positives = 314/397 (79%)

Query: 8   VERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKAL 67
           + R+ FD  MVPNYAP+  IPV+G GSR+WDQ GRE IDFAGGIAV  LGH HPALV AL
Sbjct: 3   INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSAL 62

Query: 68  TEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVY 127
           TEQAQ++WH+SN  TNEPAL LA+ LVD TFAE+V+ ANSGAEANEAA KL RR A + +
Sbjct: 63  TEQAQKLWHLSNTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKF 122

Query: 128 GPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKT 187
           G  K +IIA    FHGRTLFTV+VGGQP YSDGFGPK   I H  YN+L++LKA ISD+T
Sbjct: 123 GADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRT 182

Query: 188 CAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVV 247
           CAVVLEP+QGEGG++     +++G R+LCD+HNALLVFDEVQ+G+GR GEL+AYM  GV 
Sbjct: 183 CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVT 242

Query: 248 PDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEV 307
           PD+L++AK+LGGGFPIGAMLTT E+AKHL VGTHG+TYGGNPLA AV  AA   +NTPEV
Sbjct: 243 PDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEV 302

Query: 308 LDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVM 367
           L+GVK + + F+  L  I  +Y +F E+RG GLL+GAAL  ++ GKARD + AA +E V+
Sbjct: 303 LNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVL 362

Query: 368 VLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404
           +L A  +VVRFAPSL+I +A++ EGL RF+ A+AKLV
Sbjct: 363 LLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLV 399


Lambda     K      H
   0.318    0.135    0.394 

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: 527
Number of extensions: 12
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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:

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:

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:

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:

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