GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Jannaschia aquimarina GSW-M26

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_043918626.1 jaqu_RS08900 aspartate aminotransferase family protein

Query= reanno::WCS417:GFF4238
         (406 letters)



>NCBI__GCF_000877395.1:WP_043918626.1
          Length = 394

 Score =  332 bits (851), Expect = 1e-95
 Identities = 182/386 (47%), Positives = 238/386 (61%), Gaps = 9/386 (2%)

Query: 20  NYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSN 79
           N AP AF  V GEGS + ++ GR  +D   GIAVNVLGHAHPAL  ALT QA +LWH SN
Sbjct: 10  NRAPLAF--VSGEGSWLVERGGRRYLDLGAGIAVNVLGHAHPALTEALTAQAGQLWHTSN 67

Query: 80  VFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALN 139
           ++       LA +L++ATFA+ VFF NSG EA E A K+AR+  +   G ++  I+A   
Sbjct: 68  LYEIPQQQELAERLVEATFADTVFFTNSGTEACELAVKMARKY-WSTKGEDRATIVAFTG 126

Query: 140 SFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVS-DKTCAVVLEPIQGE 198
           SFHGR+   +   G  K +DGFGP + G  HVP+ D DA    +  D   AV+LEPIQGE
Sbjct: 127 SFHGRSSAGIAAAGSKKMTDGFGPLLPGFVHVPFGDHDAFAEVMKRDDIAAVILEPIQGE 186

Query: 199 GGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLG 258
           GG++P     L+G RD+CD   AL++ DEVQ GMGR+G LFA++  GVTPDI+  AK +G
Sbjct: 187 GGIVPVPDQCLKGLRDVCDRTGALMILDEVQCGMGRTGKLFAHEWAGVTPDIMMVAKGIG 246

Query: 259 GGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLF 318
           GGFP+ A+L TE  A  +  GTHG+TYGGNPLACAV  AV++V+     LA V  K  L 
Sbjct: 247 GGFPLGALLATEHAAAGMSAGTHGSTYGGNPLACAVGNAVMEVVADEAFLAEVRRKAGLL 306

Query: 319 KARLE-QIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVR 377
           +  LE  +     +F  VRG GL+LG       +    DV  AA    ++I+ A  +  R
Sbjct: 307 RQGLEGLVASHPDVFEVVRGSGLMLGL----KCRVPVGDVIAAARDAEVLIVPAADETAR 362

Query: 378 FAPSLVVEDADIKEGLDRFERAVKAL 403
             P+L + D DI+E LDR +RA  A+
Sbjct: 363 LLPALNIGDDDIREALDRLDRAAAAV 388


Lambda     K      H
   0.320    0.137    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: 443
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 394
Length adjustment: 31
Effective length of query: 375
Effective length of database: 363
Effective search space:   136125
Effective search space used:   136125
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)

This GapMind analysis is from Sep 24 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:

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