Aligments for a candidate for fadA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadA in Shewanella oneidensis MR-1

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 202205 SO3088 fatty oxidation complex, alpha subunit (NCBI ptt file)

Query= BRENDA::Q64428
         (763 letters)



>lcl|FitnessBrowser__MR1:202205 SO3088 fatty oxidation complex,
           alpha subunit (NCBI ptt file)
          Length = 707

 Score =  563 bits (1451), Expect = e-164
 Identities = 318/717 (44%), Positives = 441/717 (61%), Gaps = 29/717 (4%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           +A++ ++ P   +NTL  E   E  E+++EI  +  IR  VLIS K   FVAGADI+ML 
Sbjct: 16  IAILTMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDSFVAGADISMLD 75

Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168
           +C T  +A  +SQ+G  +F +LE    PVVAAI G+CLGGGLELA+AC  R+ + D KT+
Sbjct: 76  ACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACHQRVCSDDGKTM 135

Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228
           LGVPEV LG+LPG GGTQRLP++VG+  A DMMLTG+ IR  +A KMGLV+ +V      
Sbjct: 136 LGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGLVNDVVP----- 190

Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288
                 +TI  L + AV  A  LA ++++    K L+ +L        F R  ++    +
Sbjct: 191 ------QTI--LLQTAVEMA--LAGKQIAKPVKKSLVNQLLEGT---GFGRNIIFDQAAK 237

Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348
           +V K+T+G YPAP KIID V+ G+ +G   G   E+  F EL ++KES+AL  ++     
Sbjct: 238 QVAKKTQGNYPAPAKIIDCVRQGIAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTE 297

Query: 349 CKKNKF--GAPQKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405
            KK     GA  + V++  ILG GLMG GIA V+  K  +   +KD    GL       +
Sbjct: 298 MKKETGAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAY 357

Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465
           K L+  VK++ +T   RD++ + +    +YKG + AD+V+EAVFEDLA+KH+++K++E  
Sbjct: 358 KLLDKGVKRRHMTPAARDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERE 417

Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525
             EH IFASNTS+LPI QIA  + RPE VIG+HYFSPV+KM L+E+I   KTS +T A+ 
Sbjct: 418 CGEHTIFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATT 477

Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585
           VA   KQGK  IVV+DG GFY  R LA  M+E  ++L EG   + LD     FGFPVG  
Sbjct: 478 VAFARKQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALVKFGFPVGPI 537

Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645
           TL DEVGIDV   ++  L K  GERF   +      ++S    GRK+GKGFY Y + SK 
Sbjct: 538 TLLDEVGIDVGAKISPILEKELGERFKAPAA--FDKLLSDDRKGRKNGKGFYQYGAASKK 595

Query: 646 KNLNSEIDNILVNLRLPAKPEVSSD-EDIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704
           K ++  +  +     L  KP V  +   +  R + + +NEAV CL  GI+A+P +GDIGA
Sbjct: 596 KAVDETVYGV-----LGIKPGVDKEMSAVAERCVVQMLNEAVRCLDAGIIASPRDGDIGA 650

Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKF 761
           +FG+GFPP LGGPF ++D  GA  +V  L +Y++ YG +F PCQ L+ +A   ++ F
Sbjct: 651 IFGIGFPPFLGGPFHYIDTLGADNLVKILERYQTQYGDRFEPCQRLKAMAAEKARFF 707


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: 1167
Number of extensions: 53
Number of successful extensions: 5
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: 707
Length adjustment: 40
Effective length of query: 723
Effective length of database: 667
Effective search space:   482241
Effective search space used:   482241
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources