GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Desulfoscipio geothermicus DSM 3669

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase

Query= reanno::Marino:GFF3099
         (404 letters)



>NCBI__GCF_900115975.1:WP_207545101.1
          Length = 434

 Score =  213 bits (542), Expect = 9e-60
 Identities = 141/411 (34%), Positives = 222/411 (54%), Gaps = 42/411 (10%)

Query: 28  RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTN-EPALR 86
           + +G+ I D EG+E+ID  GGI     GH    +V A+ +QAEK+ H   ++T  EP L 
Sbjct: 30  KAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLLHTCFMVTMYEPYLD 89

Query: 87  LAKTLCDLT---FAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143
           LA+ L +LT   F +RV F NSGAE  E A K+AR YA      ++  IISF+ +FHGRT
Sbjct: 90  LAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYA------KRTGIISFECAFHGRT 143

Query: 144 LFTVSVGGQPK-YLEGFEP-APG---------------------GIHHAEFNDLESVKKL 180
           L T+S+  + K Y  GF P AP                      G+H  E  D     + 
Sbjct: 144 LMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRSTYPECGLHCLEQFDRMFAAE- 202

Query: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240
           +  E   A+++EP+QGEGG +     FL GLR +CD++  +L+ DEVQ+G GR+G  +A 
Sbjct: 203 VPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGIILIADEVQTGFGRTGKMFAC 262

Query: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300
           + +G+ PD+++ AK +  G P++A++  A +  +   G  G TY GN ++CA     +D 
Sbjct: 263 EHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIGGTYSGNPVSCAAGLATIDF 322

Query: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGK--AKD--- 355
           + Q  +++      DK ++ M+ + E+Y +  +VRG G +    L +    K  AK+   
Sbjct: 323 MQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLGAMNAMELVKDRNTKEPAKEETA 382

Query: 356 -FLNAGLEEGVMVLVAG--ANVIRLAPSLIIPEPDIELALERFEAAVKKLT 403
             +   ++ GV+V+ AG  +NV+R    L+I +  +E  L+  E AV  ++
Sbjct: 383 AVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDVLEQAVASVS 433


Lambda     K      H
   0.318    0.137    0.406 

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: 464
Number of extensions: 27
Number of successful extensions: 5
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: 404
Length of database: 434
Length adjustment: 32
Effective length of query: 372
Effective length of database: 402
Effective search space:   149544
Effective search space used:   149544
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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