GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Flavobacterium beibuense F44-8

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>NCBI__GCF_000769915.1:WP_035131541.1
          Length = 562

 Score =  114 bits (286), Expect = 4e-30
 Identities = 77/215 (35%), Positives = 122/215 (56%), Gaps = 14/215 (6%)

Query: 16  YRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE 75
           + +D + +A++ VS ++YEGE L +VG +G GKSTL  A+  L    +G I   G  LT+
Sbjct: 321 FGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQLDKATAGSILYKGQDLTK 380

Query: 76  ES---VWEVRKKIGMVFQNPDNQF-----VGTTVRDDV-AFGLENNGVPREEMIERVDWA 126
            S   + E+RK+I ++FQ+P +       VG  + + +   GL  N   R E    +   
Sbjct: 381 LSASAIRELRKEIQIIFQDPYSSLNPRITVGKAIMEPMKVHGLYKNDRERREKTIEI--- 437

Query: 127 VKQVNM-QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETV 185
           +K+V + ++  ++ PH  SGGQ+QRV IA  IA +P +I+ DE+ S LD   + +VL  +
Sbjct: 438 LKRVGLGEEHFNRYPHEFSGGQRQRVGIARTIALQPKLIVCDESVSALDISVQAQVLNLL 497

Query: 186 RHLKEQGMATVISITHDLNEAA-KADRIIVMNGGK 219
             LKE    T I I+HDL      +D+++VMN G+
Sbjct: 498 NELKENFGFTYIFISHDLAVVKYMSDQVLVMNKGQ 532



 Score = 94.7 bits (234), Expect = 4e-24
 Identities = 74/248 (29%), Positives = 129/248 (52%), Gaps = 24/248 (9%)

Query: 4   NQLISVEDIVFRYRKDAERRAL-DGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPE 62
           + L+++  I    RK+ +   +    +  + + E L IVG +GSGKS  + A+ GL LP+
Sbjct: 3   DSLLNINHITISARKEGQWTPIVHDSTFTLEQNEILGIVGESGSGKSVTSLAVMGL-LPK 61

Query: 63  S------GDIEVAGIQLTEESVWEVRK----KIGMVFQNPDNQF-----VGTTVRDDVAF 107
                  G I   G  +++ +  E+R      I M+FQ P +        G  V +    
Sbjct: 62  GILQVTQGSIAFEGRDISQLTTREMRNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFK- 120

Query: 108 GLENNGVPREEM---IERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDII 164
             E+  + + E+   +  +   VK  N +   ++ PH +SGGQKQRV IA  IA +P I+
Sbjct: 121 --EHTSLSKREIKATVLSLFEKVKLPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKIL 178

Query: 165 ILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAE 223
           I DE T+ LD   ++E++  ++ L+++   ++I I+HDL+  ++ A+R++VM  G    +
Sbjct: 179 IADEPTTALDVTVQKEIILLLKELQQETKMSIIFISHDLSLVSEIANRVLVMYKGNIVEQ 238

Query: 224 GPPEEIFK 231
           G   EIF+
Sbjct: 239 GVATEIFE 246


Lambda     K      H
   0.316    0.135    0.383 

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: 347
Number of extensions: 23
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 281
Length of database: 562
Length adjustment: 31
Effective length of query: 250
Effective length of database: 531
Effective search space:   132750
Effective search space used:   132750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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