GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Echinicola vietnamensis KMM 6221, DSM 17526

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate Echvi_1073 Echvi_1073 Acyl-CoA dehydrogenases

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2985
         (383 letters)



>FitnessBrowser__Cola:Echvi_1073
          Length = 599

 Score =  232 bits (592), Expect = 2e-65
 Identities = 145/393 (36%), Positives = 221/393 (56%), Gaps = 27/393 (6%)

Query: 5   ELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWID--DGLVAKMGELGLLGMVVPEEWGG 62
           E +EEQ M+    +DF   EI P ++  +     D    ++ K GELGLLG+ VPEE+ G
Sbjct: 28  EFTEEQRMMAQACQDFIDTEILPKSEEIDSMKNPDLVPAILKKAGELGLLGISVPEEYQG 87

Query: 63  TYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLNYGSEEQKQTWLADLASGQVIG 122
             + +    L  + I A  G+       H  +G  P+L YG+EEQK+ +L  LA+G+   
Sbjct: 88  LGMSFNTSMLIADIIGAA-GSFSTTYGAHTGIGTLPILYYGTEEQKKKYLPKLATGEWAA 146

Query: 123 CFCLTEPQAGSEAHNLRTRAEL-RDGQ-WVINGAKQFVSNGKRAKLAIVFAVTDPDLGKR 180
           C+CLTEP AGS+A++ +T+A L  DG+ +++NG K ++SNG  A L IVFA    D   +
Sbjct: 147 CYCLTEPDAGSDANSGKTKATLTEDGKHYLLNGQKMWISNGGFADLFIVFAKIGED---K 203

Query: 181 GISAFLVPTDTAGFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNL 240
            ++AF+V  D  G  ++  E KMGI+ S T  V  N+C +P  N+L +R  G  IA++ L
Sbjct: 204 NLTAFIVEKDFGGITMNEEEKKMGIKGSSTRQVFFNDCKVPVENMLSDRQNGFKIAVNIL 263

Query: 241 EGGRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHM--------- 291
             GR+ + A  LG  R   + AL YS +R QFG +IN   +I + LA+M +         
Sbjct: 264 NIGRVKLGAGVLGGCRQVIKNALQYSSERKQFGVSINTFGAIKSKLAEMAVKTYVSESLC 323

Query: 292 ---------QLNAARLMILHAARLRTAG-KPCLSEASQAKLFASEMAEKVCSSAIQIHGG 341
                    +++A     + A + +  G +    E + AK+  SE+ + V    +QI+GG
Sbjct: 324 YRLGQNIEDRIDALMASGMEANQAKLKGVEQFAMECAIAKIHGSEVLDYVVDQGVQIYGG 383

Query: 342 YGYLEDYPVEKYYRDARITQIYEGSSEIQRMVI 374
            GY  D P+E+ YRDARI++IYEG++EI RM++
Sbjct: 384 MGYSADAPMERAYRDARISRIYEGTNEINRMLM 416



 Score = 27.3 bits (59), Expect = 0.001
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 272 FGKAINEHQSIANLLADMHMQLNAARLMILHAARLRT--AGKPCLSEASQAKLFASEMAE 329
           FG  I E Q I   LAD+ +++ AA   +L   +  T    + C  + +  K++ +E  +
Sbjct: 482 FGPKIEEEQEIMMNLADIMIEIYAAESALLRTEKRVTLQGEEACKQQIAMVKVYLTEAVD 541


Lambda     K      H
   0.319    0.134    0.393 

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: 496
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 383
Length of database: 599
Length adjustment: 34
Effective length of query: 349
Effective length of database: 565
Effective search space:   197185
Effective search space used:   197185
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: 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