GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Shewanella loihica PV-4

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2991
         (396 letters)



>FitnessBrowser__PV4:5208388
          Length = 391

 Score =  201 bits (510), Expect = 4e-56
 Identities = 131/379 (34%), Positives = 198/379 (52%), Gaps = 17/379 (4%)

Query: 14  LGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAM 73
           L ED   +RD V D+AQ ++  R    ++++ F  ++  ++G+LG+LG T+PE YG A  
Sbjct: 18  LSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGELGLLGATLPEAYGCANA 77

Query: 74  GYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALA 133
            Y+++ +   EI R  +    +    S+L ++ I   GNE Q+ KYL KL +GE VG   
Sbjct: 78  NYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQRQKYLPKLATGEWVGCFG 137

Query: 134 MSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAF 193
           ++EP  GSD   MK +AE   G Y LNG+KMWITN P AD  VV+AK +       +  F
Sbjct: 138 LTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFVVWAKLDGV-----IRGF 192

Query: 194 LIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERA 253
           ++EKGMKG S  +   K  +R S TGE+V  +VEV  E +L  + +G K     L+  R 
Sbjct: 193 ILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEEALLPNV-EGLKGPFGCLNKARY 251

Query: 254 VLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAK 313
            +  G LG  +        Y  DR QF + +   QLIQ K+ADM T +  G  FA   A 
Sbjct: 252 GIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEITTG-LFACLQAG 310

Query: 314 NL---DMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDA 370
            L   D L  + +  ++++          KA  +A     ++GGNG  +E+ + R   + 
Sbjct: 311 RLMDQDALPVEAISLIKRNSCG-------KALEIARTSRDMHGGNGISDEFHVIRHVMNL 363

Query: 371 KLYEIGAGTSEIRRMLIGR 389
           +      GT +I  +++GR
Sbjct: 364 EAVNTYEGTHDIHALILGR 382


Lambda     K      H
   0.318    0.136    0.400 

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: 372
Number of extensions: 17
Number of successful extensions: 4
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: 396
Length of database: 391
Length adjustment: 31
Effective length of query: 365
Effective length of database: 360
Effective search space:   131400
Effective search space used:   131400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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