GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Shewanella halifaxensis HAW-EB4

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_041416449.1 SHAL_RS13845 fatty acid oxidation complex subunit alpha FadJ

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000019185.1:WP_041416449.1
          Length = 706

 Score =  803 bits (2074), Expect = 0.0
 Identities = 402/708 (56%), Positives = 527/708 (74%), Gaps = 7/708 (0%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKP 62
           M   F L  R D IA++T+DVPGE MNTL++EF  ++  ++ +++ +  ++G+V VS K 
Sbjct: 1   MEKTFNLTRRDDGIAILTMDVPGETMNTLRSEFGPEISDVLAEIKADTSIKGLVLVSGKK 60

Query: 63  DNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALA 122
           D+F+AGADI+M+  C+TA +A+ L++QG  +  E+ +LPI V+AAI+GACLGGGLELALA
Sbjct: 61  DSFVAGADISMLDACETATDAKQLSQQGHVVFNELESLPIPVVAAINGACLGGGLELALA 120

Query: 123 CHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKL 182
           CH RVC+ +PKT++G+PEVQLGLLPG GGTQRLPRL+GV+TAL+M+LTGKQLR KQALK+
Sbjct: 121 CHKRVCSLNPKTMMGVPEVQLGLLPGGGGTQRLPRLVGVTTALDMMLTGKQLRPKQALKM 180

Query: 183 GLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAGP-LGRALLFKMVGKKTEHK 239
           GLVDD VP SILL  AVE  LA K     +      ++L G   GR ++F   GK+   K
Sbjct: 181 GLVDDAVPESILLRTAVEMALAGKRPAKKKHQSFFNKVLEGTSAGRNIIFDQAGKQVAKK 240

Query: 240 TQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDP 299
           TQGNYPA  +I++ V  G+ +G + G + EA  F +L M+ +S A+RS+FFA+T++KK+ 
Sbjct: 241 TQGNYPAPAKIIDCVRQGMTKGMAKGLEVEASHFADLVMSKESGAMRSVFFATTEMKKET 300

Query: 300 GS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358
           G+ D  P  +N V +LGGGLMGGGIA VT  KA IP R+KDI+  G+++AL Y++  L+ 
Sbjct: 301 GAGDVEPQKVNKVMVLGGGLMGGGIASVTTTKAKIPARVKDISETGLSNALAYAYKLLDK 360

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

Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478
           IFASNTSSLPIG IA  A+RPE VIGLH+FSPVEKMPLVE+I H  TSA+TIATTV  AK
Sbjct: 421 IFASNTSSLPIGQIAEAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSAETIATTVAFAK 480

Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538
           KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ VEH+D AL+KFGFPVGP+ LLDE
Sbjct: 481 KQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALIKFGFPVGPMTLLDE 540

Query: 539 VGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVD 598
           VGID G KI P+LE   GERF AP      +L DDRKGRKNG+GFYLYG  G+K  K+VD
Sbjct: 541 VGIDVGAKISPILEKELGERFKAP-TAFDKLLADDRKGRKNGKGFYLYG--GKKKAKEVD 597

Query: 599 PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPF 658
             +Y ++G +      A +VA+RCV+ MLNEAVRC++E +I   RDGDIGA+FGIGFPPF
Sbjct: 598 QTVYSVLGLKPGVDTEATEVAQRCVVQMLNEAVRCLEESIIACPRDGDIGAIFGIGFPPF 657

Query: 659 LGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           LGGPF YID+LGA  +V I++   ++YGSRF P  +L +M   G  F+
Sbjct: 658 LGGPFHYIDTLGAANLVKILENYQSRYGSRFEPAAKLKQMAEEGTRFF 705


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: 1163
Number of extensions: 61
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: 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 24 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