GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Desulfovibrio vulgaris Miyazaki F

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)

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



>FitnessBrowser__Miya:8499751
          Length = 459

 Score =  169 bits (429), Expect = 1e-46
 Identities = 127/431 (29%), Positives = 207/431 (48%), Gaps = 57/431 (13%)

Query: 22  GSIIPVRGEGSRIWDQEGREFIDL-QGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMT 80
           G +I V GEG  + D  G+E++D   GG+    +G+    +  A+++Q + + + +    
Sbjct: 34  GPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAVYEQMKAMPYYAATAG 93

Query: 81  NEPALRLA-KTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSF 139
           N P +  A K L  +    R + +NSG+EANE A+K+ R  A       K +I+     +
Sbjct: 94  NIPYIEFAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKILFRARDY 153

Query: 140 HGRTLFTVSVGGQPKYLEGFEP-APGGI-------HHAEFN------DLE---SVKKLIS 182
           HG TL  +S  GQ +  E F P  PG +       +   FN      D++   +V+++I 
Sbjct: 154 HGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCARAVERIIE 213

Query: 183 KE---KTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYA 239
           +E       ++VEPI   GGV+P    +   L D+C  +  LL+ DEV  G+GR+G  + 
Sbjct: 214 QEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTGTMFG 273

Query: 240 YQMYGVVPDILSSAKGLGGGF-PVAAMLTTAKV--------AASLGVGTHGSTYGGNALA 290
           YQ YGV PDI++ AKG+   + P++   TT +V        A  +      STYGG A  
Sbjct: 274 YQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGGCAAG 333

Query: 291 CAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQ 350
           C+ A   +  + + ++L  V A  D L  G+ ++G+   V  +VRG GLL G  L +   
Sbjct: 334 CSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGDLPYV-GDVRGKGLLCGIELVQDKA 392

Query: 351 GKAKDFLNAGLEEGVMVLVAGA-------------------NVIRLAPSLIIPEPDIELA 391
           GK        + EG ++ V G                    N+I +AP+ ++   +I++ 
Sbjct: 393 GKKP------MAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNIDVI 446

Query: 392 LERFEAAVKKL 402
           L    AA+ K+
Sbjct: 447 LRTLRAALVKV 457


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: 472
Number of extensions: 35
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: 459
Length adjustment: 32
Effective length of query: 372
Effective length of database: 427
Effective search space:   158844
Effective search space used:   158844
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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