GapMind for catabolism of small carbon sources

 

Alignments 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.

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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