GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Marinobacter adhaerens HP15

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate GFF1026 HP15_1005 acyl-CoA dehydrogenase domain protein

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>FitnessBrowser__Marino:GFF1026
          Length = 389

 Score =  274 bits (701), Expect = 3e-78
 Identities = 141/360 (39%), Positives = 225/360 (62%), Gaps = 1/360 (0%)

Query: 17  FAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALEEIAA 76
           FA   + P A E DR + FP +   +M ++G  G+ V E++GG D GYLA+ +A+EEI+ 
Sbjct: 26  FAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDMGYLAHVIAMEEISR 85

Query: 77  GDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAGSDASSLK 136
              +       H+++    I + G ++QK+++L  L SG  +GA A++EP AGSD  S+K
Sbjct: 86  ASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEHIGALAMSEPNAGSDVISMK 145

Query: 137 TRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSPGYKVARV 196
             A+  GDHY+LNG K +IT+G +A   +++A TD SAG RG++AFIV  D+PG+   + 
Sbjct: 146 LTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGVTAFIVERDAPGFSRHQK 205

Query: 197 EDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSVGMARAAF 256
            DKLG   S+TC+++F+D +VP  N LG  G G K+ ++ L+  R+ ++   +G+ +AA 
Sbjct: 206 LDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDYERLVLSGGPLGIMQAAM 265

Query: 257 EAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSG-KPALVEAS 315
           +    Y RER+ FG+ I E + V  ++ADM T +  A+  V+  A   D G +    +A+
Sbjct: 266 DVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYMVAMSADRGAETTRKDAA 325

Query: 316 MAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL 375
            A L+++EMA K+   A+Q LGG GY++++P  R+ RD ++ +I  GTS+I+RM+I R L
Sbjct: 326 GAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAKLYEIGAGTSEIRRMLIGREL 385


Lambda     K      H
   0.319    0.134    0.389 

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: 332
Number of extensions: 14
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: 389
Length adjustment: 30
Effective length of query: 345
Effective length of database: 359
Effective search space:   123855
Effective search space used:   123855
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.

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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