GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Stutzerimonas stutzeri A1501

Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011913066.1 PST_RS09725 acyl-CoA dehydrogenase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983
         (375 letters)



>NCBI__GCF_000013785.1:WP_011913066.1
          Length = 383

 Score =  441 bits (1134), Expect = e-128
 Identities = 216/372 (58%), Positives = 277/372 (74%)

Query: 4   NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTG 63
           ++DQ+ IRDMARDFA+  + P A  W++        + +M  LG  GM+VPE+WGG    
Sbjct: 7   SEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDALVAQMGELGLLGMVVPEEWGGSYID 66

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFAL 123
           Y+AYA+A+EEI+AGDGA   +MS+HNSVGC P+LNYG+  QK+ +L  LASG  +G FAL
Sbjct: 67  YVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLAELASGRAIGCFAL 126

Query: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEPQAGS+A  L+TRA L    +VLNG KQF ++ + A + IVFAVTDP  GK+G+SAF+
Sbjct: 127 TEPQAGSEAHNLRTRAELVDGQWVLNGSKQFCSNAKRAKLAIVFAVTDPDLGKKGLSAFL 186

Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243
           VPTD+ G+ V R E K+G  ASDTC +   D ++P AN LGE G+G  IAL+NLEGGR+G
Sbjct: 187 VPTDTAGFAVERSEHKMGIRASDTCAVSLSDCRIPQANLLGERGKGLAIALSNLEGGRIG 246

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           I +Q++G+ARAAFEAA  YARER  FGKPI EHQ++A  LADM TQ+  AR ++ +AA L
Sbjct: 247 IGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARL 306

Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGT 363
           + +G P L EAS AKLFASEMAEKVCS A+Q  GGYGYL D+PVER YRD R+ QIYEG+
Sbjct: 307 KSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGS 366

Query: 364 SDIQRMVISRNL 375
           S+IQR++I+R L
Sbjct: 367 SEIQRLLIAREL 378


Lambda     K      H
   0.320    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: 420
Number of extensions: 11
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: 375
Length of database: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
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 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