GapMind for catabolism of small carbon sources

 

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

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__PV4:5209977
          Length = 706

 Score =  563 bits (1450), Expect = e-164
 Identities = 318/718 (44%), Positives = 445/718 (61%), Gaps = 28/718 (3%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           +AV+ ++ P   +NTL  E   E  E++ EI A+  IR  V+IS K   FVAGADI+ML 
Sbjct: 14  IAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLD 73

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

Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228
           LG+PEV LG+LPG GGTQRLP++VG+  + DMMLTG+ +RA +A KMGLVD +V      
Sbjct: 134 LGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVV------ 187

Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288
              PE   ++   E+A      LA  + + K     +EKL       P  R  +++   +
Sbjct: 188 ---PESILLQTAIEMA------LAGARPAKKPKLSTVEKLLEGT---PVGRNIIFEQALK 235

Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348
           +V K+T+G YPAP KIID V+ G+ +G   G   E++ FG+L ++ ES+AL  ++     
Sbjct: 236 QVNKKTQGNYPAPEKIIDCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTE 295

Query: 349 CKKNKFGAP--QKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405
            KK         K V ++ +LG GLMG GIA V+  K  +   +KD +  GL       +
Sbjct: 296 MKKESGAGDVSPKAVNKVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAY 355

Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465
           K L   VK++ +T   RD++ + +    +YKG + ADMV+EAVFEDL +KH+++K+VE  
Sbjct: 356 KLLAKGVKRRHMTPAVRDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERE 415

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

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

Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645
           TL DEVGIDV   ++  L K  GERF   +      +++    GRK+GKGFY Y + SK 
Sbjct: 536 TLLDEVGIDVGAKISPILEKELGERFKAPAA--FDKLLADDRKGRKNGKGFYQYGAKSKK 593

Query: 646 KNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAV 705
           K ++  +  +L  L   A  E  +   +  R + + +NEAV CL+EGI+A+P +GDIGA+
Sbjct: 594 KLVDESVYGVL-GLTPGADGEPIA---LAERCVVQMLNEAVRCLEEGIIASPRDGDIGAI 649

Query: 706 FGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763
           FG+GFPP LGGPFR++D  GA+ +V+ L++Y+  +G +F PC  L ++A + S KFY+
Sbjct: 650 FGIGFPPFLGGPFRYMDSLGAKHLVETLKRYQDQFGDRFAPCDRLVEMAESGS-KFYE 706


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: 1212
Number of extensions: 60
Number of successful extensions: 7
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: 706
Length adjustment: 40
Effective length of query: 723
Effective length of database: 666
Effective search space:   481518
Effective search space used:   481518
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