GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Shewanella sp. ANA-3

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 7024806 Shewana3_1984 acyl-CoA dehydrogenase domain-containing protein (RefSeq)

Query= BRENDA::P26440
         (426 letters)



>FitnessBrowser__ANA3:7024806
          Length = 585

 Score =  120 bits (301), Expect = 1e-31
 Identities = 111/378 (29%), Positives = 174/378 (46%), Gaps = 44/378 (11%)

Query: 84  WKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGL--SYGAHSNLCINQLV 141
           + Q    G +G+    ++GG G+  +  VLV E    A  A  L  S  A + LCIN   
Sbjct: 84  YDQYSQGGWVGLCGEPEFGGMGMPKMLGVLVDEMAYSACNAFTLYGSLTAGAALCINA-- 141

Query: 142 RNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKA-EKKGNHYILNGNKFWIT 200
            +G+E  KE YLPKL SGE+ GA+ M+EP AGSD+ +++ +A  +    Y ++G+K +IT
Sbjct: 142 -HGSEEIKETYLPKLYSGEWAGAMDMTEPQAGSDLRNIRTRAIPQDDGSYAISGSKIFIT 200

Query: 201 NGPDADVLIVYAKTDLAAVPASRGITAFIVEK----------GMPGFSTSKKLDKLGMRG 250
            G D D+        LA +P S+GI+ F+V K             G S      K+G++G
Sbjct: 201 GG-DHDLTENVIHLVLAKLPESKGISLFLVPKTTVNADGSLGQANGVSVGSIEHKMGLKG 259

Query: 251 SNTCELIFEDCKIPAANILGHENKGVYVLMSGLDLERLVLAGGPLGLMQAVLDHTIPYLH 310
           S TC + F++ K     ++G  N+G+  + + ++ ERL +    LG  QA       Y  
Sbjct: 260 SATCVMNFDEAK---GYLIGEPNRGLVCMFTMMNYERLAIGIQGLGSAQAAYQMAADYAK 316

Query: 311 VRE----AFGQKIGHFQ---LMQGKMADMYTRLMAC----RQYVYNVAKACD-----EGH 354
            R     A G   G      ++ G +  M   + A     R       K  D     EG 
Sbjct: 317 ERNQGVAAGGSPTGSDSDPIIVHGDVRRMLLTIRAMTEAGRALSVFTGKQLDLAKYAEGE 376

Query: 355 CTAKDCAGVILYSAECATQVALDGI-------QCFGGNGYINDFPMGRFLRDAKLYEIGA 407
             AK    V L +      +   G+       Q FGG+GYI +  + + +RD ++ +I  
Sbjct: 377 VKAKAARYVGLLTPVAKAFLTDRGLDATIMAQQVFGGHGYIRETGIEQLVRDTRIAQIYE 436

Query: 408 GTSEVRRL-VIGRAFNAD 424
           GT+ ++ +  +GR    D
Sbjct: 437 GTNGIQAIDFLGRKVTGD 454


Lambda     K      H
   0.321    0.137    0.410 

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: 521
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 585
Length adjustment: 34
Effective length of query: 392
Effective length of database: 551
Effective search space:   215992
Effective search space used:   215992
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: 52 (24.6 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