GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Shewanella sp. ANA-3

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 7024269 Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= CharProtDB::CH_003230
         (714 letters)



>lcl|FitnessBrowser__ANA3:7024269 Shewana3_1461 multifunctional
           fatty acid oxidation complex subunit alpha (RefSeq)
          Length = 709

 Score =  813 bits (2100), Expect = 0.0
 Identities = 408/710 (57%), Positives = 529/710 (74%), Gaps = 7/710 (0%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKP 62
           M   F L  R D IA++ +DVPGE MNTLKAEF  ++  I+ +++ +  +RG+V +S K 
Sbjct: 1   MEKTFNLTRREDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKK 60

Query: 63  DNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALA 122
           D+F+AGADI+M+  C+TA +A+AL++QG  +  E+ AL I V+AAIHGACLGGGLELALA
Sbjct: 61  DSFVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALA 120

Query: 123 CHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKL 182
           CH RVC+DD KT+LG+PEVQLGLLPG GGTQRLPRL+G++TAL+M+LTGKQ+R KQALK+
Sbjct: 121 CHQRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKM 180

Query: 183 GLVDDVVPHSILLEAAVELAKKERPSSRPLP---VRERILAGPLGRALLFKMVGKKTEHK 239
           GLV+DVVP +ILL+ AVE+A   + +++P+    V + +     GR ++F    K+   K
Sbjct: 181 GLVNDVVPQTILLQTAVEMALAGKRTAKPVKKSLVNQLLEGTGFGRNIIFDQAAKQVVKK 240

Query: 240 TQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDP 299
           TQGNYPA  +I++ V  G+A+G   G + EA  F EL ++ +S+ALRSIFFA+T++KK+ 
Sbjct: 241 TQGNYPAPAKIIDCVRQGMAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTEMKKET 300

Query: 300 GSD-APPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358
           G++ A P  +    ILGGGLMGGGIA VT  KA IP R+KDIN +G+++AL Y++  L+ 
Sbjct: 301 GAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAYKLLDK 360

Query: 359 KVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418
            V+RRH+  + RD  +AL++ TT+Y+G    D+++EAVFE+L LK QMV ++E+ C  HT
Sbjct: 361 GVKRRHMTPAVRDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERECGEHT 420

Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478
           IFASNTSSLPIG IA  A+RPE VIGLH+FSPVEKMPLVE+I HA TS +TIATTV  A+
Sbjct: 421 IFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATTVAFAR 480

Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538
           KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ +EH+D ALVKFGFPVGPI LLDE
Sbjct: 481 KQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSIEHLDKALVKFGFPVGPITLLDE 540

Query: 539 VGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLY--GQKGRKSKKQ 596
           VGID G KI P+LE   GERF APA     +L+DDRKGRKNG+GFY Y  G K    KK 
Sbjct: 541 VGIDVGAKIAPILEKELGERFKAPA-AFDKLLSDDRKGRKNGKGFYQYAAGNKASSKKKA 599

Query: 597 VDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFP 656
           VD ++Y ++G +         VAERCV+ MLNEAVRC+D+ +I S RDGDIGA+FGIGFP
Sbjct: 600 VDESVYAVLGIKPGMDKDLSAVAERCVVQMLNEAVRCLDDGIIASPRDGDIGAIFGIGFP 659

Query: 657 PFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           PFLGGPF YID+LGA  +V I++R   QYG RF PC RL  M A    F+
Sbjct: 660 PFLGGPFHYIDTLGADNLVNILERYQAQYGDRFEPCPRLKAMAAEKARFF 709


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: 1135
Number of extensions: 48
Number of successful extensions: 7
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: 709
Length adjustment: 39
Effective length of query: 675
Effective length of database: 670
Effective search space:   452250
Effective search space used:   452250
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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