Aligments for a candidate for paaH in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Aligments for a candidate for paaH in Shewanella loihica PV-4

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 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__PV4:5209977
          Length = 706

 Score =  815 bits (2104), Expect = 0.0
 Identities = 417/710 (58%), Positives = 538/710 (75%), Gaps = 9/710 (1%)

Query: 3   MTSAFTLNVRLDN-IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAK 61
           M  +FTLN RLDN IAV+T+DVPGE MNTL+AEF  ++  ++ +++ +  +RGVV +S K
Sbjct: 1   MDKSFTLN-RLDNGIAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGK 59

Query: 62  PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELAL 121
            D+F+AGADI+M+  C TA++A  L++QG ++   + +L I V+AAI+GACLGGGLELAL
Sbjct: 60  KDSFVAGADISMLDACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELAL 119

Query: 122 ACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALK 181
           ACH RVCTD  KT+LGLPEVQLGLLPG GGTQRLPRL+G++ +L+M+LTGKQLRAKQALK
Sbjct: 120 ACHQRVCTDSNKTMLGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALK 179

Query: 182 LGLVDDVVPHSILLEAAVELAKK-ERPSSRP-LPVRERILAG-PLGRALLFKMVGKKTEH 238
           +GLVDDVVP SILL+ A+E+A    RP+ +P L   E++L G P+GR ++F+   K+   
Sbjct: 180 MGLVDDVVPESILLQTAIEMALAGARPAKKPKLSTVEKLLEGTPVGRNIIFEQALKQVNK 239

Query: 239 KTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKD 298
           KTQGNYPA E+I++ V  G+ +G   G + EA+ FG+L ++ +S+ALRSIFFA+T++KK+
Sbjct: 240 KTQGNYPAPEKIIDCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTEMKKE 299

Query: 299 PGS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357
            G+ D  P  +N V +LGGGLMGGGIA VT  KA IPVR+KDI+  G+++AL Y++  L 
Sbjct: 300 SGAGDVSPKAVNKVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAYKLLA 359

Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAH 417
             V+RRH+  + RD  +AL++ TT+Y+G    D+++EAVFE+L LK QMV +VE+ C  H
Sbjct: 360 KGVKRRHMTPAVRDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERECGEH 419

Query: 418 TIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLA 477
           TIFASNTSSLPI  IA  A RPE VIGLH+FSPVEKMPLVE+I H  TS QTIATTV  A
Sbjct: 420 TIFASNTSSLPIKQIAEAAERPENVIGLHYFSPVEKMPLVEVIAHDKTSPQTIATTVAFA 479

Query: 478 KKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLD 537
           +KQGKTPIVV+D AGFYVNRILA Y+NEA  +L +G+ V+H+D ALVKFGFPVGP+ LLD
Sbjct: 480 RKQGKTPIVVKDGAGFYVNRILALYMNEAANLLLEGQSVDHLDKALVKFGFPVGPMTLLD 539

Query: 538 EVGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQV 597
           EVGID G KI P+LE   GERF APA     +L DDRKGRKNG+GFY YG K +  KK V
Sbjct: 540 EVGIDVGAKISPILEKELGERFKAPA-AFDKLLADDRKGRKNGKGFYQYGAKSK--KKLV 596

Query: 598 DPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPP 657
           D ++Y ++G           +AERCV+ MLNEAVRC++E +I S RDGDIGA+FGIGFPP
Sbjct: 597 DESVYGVLGLTPGADGEPIALAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPP 656

Query: 658 FLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFWK 707
           FLGGPFRY+DSLGA  +V  ++R   Q+G RF PC+RLVEM   G  F++
Sbjct: 657 FLGGPFRYMDSLGAKHLVETLKRYQDQFGDRFAPCDRLVEMAESGSKFYE 706


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: 1190
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: 714
Length of database: 706
Length adjustment: 39
Effective length of query: 675
Effective length of database: 667
Effective search space:   450225
Effective search space used:   450225
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 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