GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Shewanella amazonensis SB2B

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__SB2B:6938693
          Length = 391

 Score =  194 bits (493), Expect = 3e-54
 Identities = 123/372 (33%), Positives = 185/372 (49%), Gaps = 6/372 (1%)

Query: 2   LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61
           L+ +E++ I D V  +AQ++L       ++D  F +E ++E+ ELGL G  +PE++G ++
Sbjct: 17  LLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLPEEYGCAN 76

Query: 62  TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121
             YV+Y +   EI   D    + MSV +S+   PI  +G E Q+ ++L  LATG  +G F
Sbjct: 77  ANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLATGEWVGCF 136

Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181
            LTEP  GSD + +KTRA      Y + G+K +IT+   A V +V+A  D       I  
Sbjct: 137 GLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAKLD-----GAIRG 191

Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241
           F++     G    ++E K    AS T +IV DNV+V   + L    EG K     L   R
Sbjct: 192 FVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVG-EDALLPNVEGLKGPFGCLNKAR 250

Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301
            GIA  A+G A   +  AR Y  +R  F +PL  +Q    +LADM T+I+      L A 
Sbjct: 251 YGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFACLQAG 310

Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361
            L D     +   S+ K  +   A  +   A    GG G   +F + R   ++     YE
Sbjct: 311 RLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEAVNTYE 370

Query: 362 GTSDIQRMVIAR 373
           GT DI  +++ R
Sbjct: 371 GTHDIHALILGR 382


Lambda     K      H
   0.319    0.134    0.382 

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: 320
Number of extensions: 15
Number of successful extensions: 2
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: 375
Length of database: 391
Length adjustment: 30
Effective length of query: 345
Effective length of database: 361
Effective search space:   124545
Effective search space used:   124545
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 17 2021. The underlying query database was built on Sep 17 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