GapMind for catabolism of small carbon sources

 

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

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__ANA3:7024269
          Length = 709

 Score =  563 bits (1452), Expect = e-165
 Identities = 318/717 (44%), Positives = 442/717 (61%), Gaps = 25/717 (3%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           +A++ ++ P   +NTL  E   E  E+++EI  +  IR  VLIS K   FVAGADI+ML 
Sbjct: 14  IAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDSFVAGADISMLD 73

Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168
           +C T  +A  +SQ+G  +F +LE    PVVAAI G+CLGGGLELA+AC  R+ + D KT+
Sbjct: 74  ACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACHQRVCSDDGKTM 133

Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228
           LGVPEV LG+LPG GGTQRLP++VG+  A DMMLTG+ IR  +A KMGLV+ +V      
Sbjct: 134 LGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGLVNDVVP----- 188

Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288
                 +TI  L + AV  A  LA ++ +    K L+ +L        F R  ++    +
Sbjct: 189 ------QTI--LLQTAVEMA--LAGKRTAKPVKKSLVNQLLEGT---GFGRNIIFDQAAK 235

Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348
           +V K+T+G YPAP KIID V+ G+ +G   G   E+  F EL ++KES+AL  ++     
Sbjct: 236 QVVKKTQGNYPAPAKIIDCVRQGMAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTE 295

Query: 349 CKKNKF--GAPQKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405
            KK     GA  + V++  ILG GLMG GIA V+  K  +   +KD    GL       +
Sbjct: 296 MKKETGAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAY 355

Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465
           K L+  VK++ +T   RD++ + +    +YKG + AD+V+EAVFEDLA+KH+++K++E  
Sbjct: 356 KLLDKGVKRRHMTPAVRDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERE 415

Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525
             EH IFASNTS+LPI QIA  + RPE VIG+HYFSPV+KM L+E+I   KTS +T A+ 
Sbjct: 416 CGEHTIFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATT 475

Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585
           VA   KQGK  IVV+DG GFY  R LA  M+E  ++L EG   + LD     FGFPVG  
Sbjct: 476 VAFARKQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSIEHLDKALVKFGFPVGPI 535

Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645
           TL DEVGIDV   +A  L K  GERF   +      ++S    GRK+GKGFY Y +G+K 
Sbjct: 536 TLLDEVGIDVGAKIAPILEKELGERFKAPAA--FDKLLSDDRKGRKNGKGFYQYAAGNKA 593

Query: 646 KNLNSEIDNILVNLRLPAKPEVSSD-EDIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704
            +    +D  +  + L  KP +  D   +  R + + +NEAV CL +GI+A+P +GDIGA
Sbjct: 594 SSKKKAVDESVYAV-LGIKPGMDKDLSAVAERCVVQMLNEAVRCLDDGIIASPRDGDIGA 652

Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKF 761
           +FG+GFPP LGGPF ++D  GA  +V+ L +Y++ YG +F PC  L+ +A   ++ F
Sbjct: 653 IFGIGFPPFLGGPFHYIDTLGADNLVNILERYQAQYGDRFEPCPRLKAMAAEKARFF 709


Lambda     K      H
   0.317    0.135    0.380 

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: 1166
Number of extensions: 59
Number of successful extensions: 6
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: 763
Length of database: 709
Length adjustment: 40
Effective length of query: 723
Effective length of database: 669
Effective search space:   483687
Effective search space used:   483687
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: 55 (25.8 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