Alignments for a candidate for fadB in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Photobacterium jeanii R-40508

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_068329511.1 A3K86_RS06710 fatty acid oxidation complex subunit alpha FadJ

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_001650345.1:WP_068329511.1
          Length = 701

 Score =  836 bits (2159), Expect = 0.0
 Identities = 421/702 (59%), Positives = 528/702 (75%), Gaps = 5/702 (0%)

Query: 5   SAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDN 64
           SAF+L    + IA + +DVP EKMNTL++ FA QV A++ +L+   +++G+V  S KPDN
Sbjct: 4   SAFSLTYGDNGIAWLKVDVPDEKMNTLQSVFAEQVSAVLAELKTKSDVKGMVIHSGKPDN 63

Query: 65  FIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACH 124
           FIAGADI M+  C TA+EA+ALA QGQ+L A++  LP  V+AAIHG CLGGGLELALACH
Sbjct: 64  FIAGADIKMLAACTTAKEAQALATQGQELFAQLEQLPFHVVAAIHGPCLGGGLELALACH 123

Query: 125 GRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGL 184
            RVC+DD KT LGLPEVQLGLLPGSGGTQRLPRL+GV+ AL+MILTGKQLRAK+A KLGL
Sbjct: 124 SRVCSDDDKTRLGLPEVQLGLLPGSGGTQRLPRLVGVANALDMILTGKQLRAKKAKKLGL 183

Query: 185 VDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKTQGNY 244
           V++ VP SILLE A + A K +P  +       +   P+GR+L+F+   KKT  KT+GNY
Sbjct: 184 VEESVPLSILLEIAEKQALKPKPKRKGTMQEWALGGNPIGRSLVFEQATKKTREKTRGNY 243

Query: 245 PATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAP 304
           PATE ILEVV+ GL  G   G   EA  FGEL M+P+S ALRSIFFA+T++KK+ G+DA 
Sbjct: 244 PATEAILEVVKVGLQDGMKKGLALEAERFGELVMSPESAALRSIFFATTEMKKENGADAT 303

Query: 305 PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRH 364
           P  +  +G+LGGGLMGGGI++V+A KA +  RIKDI+  GI +AL Y++  LE + +RR 
Sbjct: 304 PLKIQRIGVLGGGLMGGGISHVSAVKAKLTTRIKDISNDGIQNALNYNYKLLEKQRKRRI 363

Query: 365 LKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNT 424
           +  ++   ++  I+G  DY GF H D++IEAVFE+L LK QMV ++E N    TIFA+NT
Sbjct: 364 ISKAQLQSKMMSITGGIDYTGFNHADVVIEAVFEDLGLKHQMVQDIEANAKPETIFATNT 423

Query: 425 SSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTP 484
           SSLPI  IA  A RPE V+GLH+FSPVEKMPLVE+IPH GTS QT+AT V LAKKQGKTP
Sbjct: 424 SSLPIHQIAQVAERPENVVGLHYFSPVEKMPLVEVIPHQGTSPQTVATVVALAKKQGKTP 483

Query: 485 IVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTG 544
           IVV DKAGFYVNRILAPY+NEA  +L  GE +EH+D AL+ FGFPVGPI LLDEVG+D G
Sbjct: 484 IVVGDKAGFYVNRILAPYMNEAASLLMAGEPIEHLDNALLDFGFPVGPITLLDEVGVDIG 543

Query: 545 TKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPL 604
            KI+P+L A  GERF  P +V  ++LND+RKGRK+G+GFYLY  K    KK+VD  +Y L
Sbjct: 544 AKIMPILVAELGERFKGP-DVFETLLNDNRKGRKSGKGFYLYDSK----KKEVDKTVYKL 598

Query: 605 IGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFR 664
           +  + Q  ++A  VA+RC ++MLNEAVRC+DE VIRS RDGDIGA+FGIGFPPFLGGPFR
Sbjct: 599 LNLEPQQHLAAIDVAQRCSLMMLNEAVRCLDEGVIRSPRDGDIGAIFGIGFPPFLGGPFR 658

Query: 665 YIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           Y+D LG   VV ++     +YG RFTPCE+LV M + G+ F+
Sbjct: 659 YMDQLGIPRVVELLNEYKDKYGERFTPCEKLVAMASEGQRFY 700


Lambda     K      H
   0.319    0.137    0.393 

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: 1126
Number of extensions: 39
Number of successful extensions: 4
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: 714
Length of database: 701
Length adjustment: 39
Effective length of query: 675
Effective length of database: 662
Effective search space:   446850
Effective search space used:   446850
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: 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 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