Aligments for a candidate for fadB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadB in Shewanella amazonensis SB2B

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 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__SB2B:6938034
          Length = 706

 Score =  823 bits (2127), Expect = 0.0
 Identities = 409/708 (57%), Positives = 544/708 (76%), Gaps = 6/708 (0%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKP 62
           M   F+L+ R D IA++T+DVPGE MNTLKA+FA ++ AI+++++ +  ++G+V +S K 
Sbjct: 1   MEKTFSLSRRDDGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKA 60

Query: 63  DNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALA 122
           D+F+AGADI+M+  C+TA++A  L+RQG  + AE+  L I V+AAIHGACLGGGLELALA
Sbjct: 61  DSFVAGADISMLDACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALA 120

Query: 123 CHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKL 182
           CH RVC+D  KT+LG+PEVQLGLLPG GGTQRLPRLIG++ AL+++LTGKQ+R KQA+K+
Sbjct: 121 CHQRVCSDSSKTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKM 180

Query: 183 GLVDDVVPHSILLEAAVELAKKERPSSRPL--PVRERILAG-PLGRALLFKMVGKKTEHK 239
           GLVDDVVP SILL+ A+E+A   + + +PL  P+  ++L G P+GR ++F    K+   K
Sbjct: 181 GLVDDVVPESILLDTAIEMALAGKKTRKPLKQPLVTKLLEGTPVGRNIMFDQATKQVLKK 240

Query: 240 TQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDP 299
           TQGNYP+  +I++ V  G+A+G   G + EA  FG L  TP+S ALRSIFFA+T++KK+ 
Sbjct: 241 TQGNYPSPLKIIDCVREGMAKGMEKGLEVEAAHFGALVATPESAALRSIFFATTEMKKET 300

Query: 300 GS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358
           G+ DA P  +    +LGGGLMGGGIA VT  KA +PVR+KDI+ +G+++AL Y++  L+ 
Sbjct: 301 GAGDAKPRKVAKAVVLGGGLMGGGIASVTTTKAKVPVRVKDISDKGLSNALGYAYKLLDK 360

Query: 359 KVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418
            V+RRH+ ++ERDK +AL++ TT+YRG    D+++EAVFE+L LK QMV ++E+ C  HT
Sbjct: 361 GVKRRHMTSAERDKLMALMTTTTEYRGVKDADIVVEAVFEDLNLKHQMVRDIERECGEHT 420

Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478
           IFASNTSSLPI  IAA A+RPE VIGLH+FSPVEKMPLVE+I H  TS +TIATTV  A+
Sbjct: 421 IFASNTSSLPITQIAAAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSPETIATTVAFAR 480

Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538
           KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ V+H+D ALVKFGFPVGP+ LLDE
Sbjct: 481 KQGKTPIVVKDCAGFYVNRILALYMNEAAQLLLEGQAVDHLDKALVKFGFPVGPMTLLDE 540

Query: 539 VGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVD 598
           VGID G KI P+LE   GERF APA     ++ DDRKGRKNG+GFYLYG+  +K KK VD
Sbjct: 541 VGIDVGAKISPILEKELGERFKAPA-AFDKLMADDRKGRKNGKGFYLYGKAAKKGKK-VD 598

Query: 599 PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPF 658
            ++Y L+G        A ++AERCV+ MLNEAVRC++E +I S RDGDIGA+FGIGFPPF
Sbjct: 599 ESVYSLLGLTPATGKEAGEIAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPPF 658

Query: 659 LGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           LGGPFRY+D+LGA ++V +++   ++YG RF P   L  M A G++F+
Sbjct: 659 LGGPFRYMDTLGAAKMVRLLEGYQSKYGDRFAPAALLKAMAAEGKTFY 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: 1125
Number of extensions: 42
Number of successful extensions: 8
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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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, 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