Alignments for a candidate for fadB in Amphritea japonica JAMM 1866

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Amphritea japonica JAMM 1866

Align FadB (EC 5.3.3.8; EC 1.1.1.35; EC 5.1.2.3; EC 4.2.1.17; EC 1.1.1.36) (characterized)
to candidate WP_019622596.1 G329_RS0113855 fatty acid oxidation complex subunit alpha FadB

Query= metacyc::G1G01-2277-MONOMER
         (715 letters)



>NCBI__GCF_000381785.1:WP_019622596.1
          Length = 715

 Score =  887 bits (2293), Expect = 0.0
 Identities = 449/715 (62%), Positives = 537/715 (75%)

Query: 1   MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIRADASVKGVIVRS 60
           M +EG+AI V+ ++SG+ EL FDL+ E VNKFN+LTL+EL+ AV  + A   +KGV+  S
Sbjct: 1   MQFEGQAIRVQKIDSGLYELIFDLQTEPVNKFNQLTLSELKDAVTQLSAVKDIKGVLFSS 60

Query: 61  GKDVFIVGADITEFVDNFKLPEAELVAGNLEANRIFNAFEDLEVPTVAAINGIALGGGLE 120
            KD FIVGADITEF   F   EA LV   LE + IFNA EDL  PTV AING+ALGGG E
Sbjct: 61  AKDSFIVGADITEFSSLFDRGEAGLVEKLLENHAIFNAVEDLPCPTVVAINGLALGGGFE 120

Query: 121 MCLAADYRVMSTSARIGLPEVKLGIYPGFGGTVRLPRLIGSDNAIEWIAAGKENRAEDAL 180
           +CLAADYRVM   A++GLPEVKLGI PG+GG VRLPRLIG DNA EWI  G E RA  AL
Sbjct: 121 LCLAADYRVMGEKAKVGLPEVKLGINPGWGGIVRLPRLIGIDNAHEWICTGVEKRAAAAL 180

Query: 181 KVGAVDAVVAPELLLAGALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240
           K GAVDAVVA E +    LDL+++   G+ DY+A+R  K   +KLN IEQMMAFETAKG 
Sbjct: 181 KDGAVDAVVAQEQVREAGLDLLRQCAEGKFDYQARRTEKQSPVKLNQIEQMMAFETAKGM 240

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFAKLAKTSVAESLIGLFLNDQEL 300
           +  +AGP+YPAP++A+K+IQK+    RD+A+  E  G AKLA   V ++L+GLF+ DQ +
Sbjct: 241 IGAKAGPHYPAPLQAVKTIQKSCGMNRDQAILAEIKGVAKLASGPVVKALVGLFMKDQYV 300

Query: 301 KRKAKAHDEIAHDVKQAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKL 360
           K+ +K H   A  V QAAVLGAGIMGGG+AYQSA KG PILMKDI E AIQLGL+EA+KL
Sbjct: 301 KKVSKGHVAKAAQVNQAAVLGAGIMGGGVAYQSASKGVPILMKDINEAAIQLGLDEANKL 360

Query: 361 LGNRVEKGRLTPAKMAEALNAIRPTLSYGDFANVDIVVEAVVENPKVKQAVLAEVEGQVK 420
           L  ++++GR   AKMA  +N IRPTLSYGDF NVD+VVEAVVENPKVKQ VLAE E  + 
Sbjct: 361 LAGQLKRGRTDAAKMAATINRIRPTLSYGDFGNVDLVVEAVVENPKVKQMVLAEAETHLA 420

Query: 421 DDAILASNTSTISINLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVA 480
           DDA+LASNTSTISIN LAK+LKRPENF GMHFFNPVH MPLVEVIRGEK+SD  +A TV+
Sbjct: 421 DDAVLASNTSTISINALAKSLKRPENFCGMHFFNPVHKMPLVEVIRGEKTSDETIARTVS 480

Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540
           YA  MGK PIVVNDCPGFLVNRVLFPYFGGF+ L+  G DF  +DKVME+FGWPMGPAYL
Sbjct: 481 YATAMGKTPIVVNDCPGFLVNRVLFPYFGGFSGLLQDGADFRNVDKVMERFGWPMGPAYL 540

Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKP 600
           +DVVGIDT HH   VMA GFP+RM  E  S +D +Y   R GQKNGKGFY YE D++GK 
Sbjct: 541 LDVVGIDTAHHADQVMAAGFPERMSHEGESVIDRMYSLERFGQKNGKGFYRYELDRKGKL 600

Query: 601 KKVFDATVLDVLKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVY 660
            K  D  V  +L+  V    E TD+ II  MM+PLC+ETVRCLE+GIV + AEADM ++Y
Sbjct: 601 AKRADDEVDALLESCVGAACEFTDQTIIERMMIPLCIETVRCLEEGIVASPAEADMAMIY 660

Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGPLYHPTAKLREMAKNGQRFFN 715
           GIGFPPFRGG   Y+D +G+A F  +  +Y  LGPLY PT K+++MA N  ++FN
Sbjct: 661 GIGFPPFRGGVFHYLDEMGLAAFCEMTAKYEALGPLYQPTEKMQQMAANATKYFN 715


Lambda     K      H
   0.319    0.137    0.388 

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: 1422
Number of extensions: 52
Number of successful extensions: 1
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: 715
Length of database: 715
Length adjustment: 39
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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