GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Tistlia consotensis USBA 355

Align ABC transporter related (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  317 bits (812), Expect = 6e-91
 Identities = 185/498 (37%), Positives = 282/498 (56%), Gaps = 9/498 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LEL+ +S+ +PGV AL+ V  +L  GEVH L GENGAGKST++ ++ GA     G+  F
Sbjct: 23  LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            GEP   N+   A+  GIS V+QE +LVP +TV +NLFLG E  RLGL+  + ++  A A
Sbjct: 83  RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L +    +     +   + A QQ++ IA+       VL+LDEPTASL  +E   LF ++
Sbjct: 143 ILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLI 202

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            Q+KA+GV +++ITH L ++ +I DRITVLR+G+++        P+ +L+  M GR   E
Sbjct: 203 EQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRVYDE 262

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDV-SVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
                  K R     E  LLS+E + +  GS+   +L+V  G+ VGLAGL+GSG+SEV  
Sbjct: 263 LF----PKVRFKPGRE--LLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVAR 316

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL--A 360
           A FGL+ +  G + L G+++    P   +  G    P DR+ +G++    +REN+ L   
Sbjct: 317 ACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSL 376

Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420
             A  G    L    + +  +   ++L +  P  ++ +E  SGGNQQKV+LA+       
Sbjct: 377 TLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQ 436

Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR 480
           +   DEPT G+D+G    I + IR LC+ G  +L+ SS+L E++  SN+  V        
Sbjct: 437 VFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQA 496

Query: 481 ELSGAELTSQHVMQAIAE 498
           EL+G E+T + V+    E
Sbjct: 497 ELAGDEITEEKVLSHFFE 514



 Score = 54.3 bits (129), Expect = 1e-11
 Identities = 59/251 (23%), Positives = 103/251 (41%), Gaps = 26/251 (10%)

Query: 6   ELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLG 65
           EL  + +      ++ + SL + AGE+  L G  G+GKS + +   G +    G +   G
Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333

Query: 66  E------PQH------FNTPMDAQKAGIST---VYQEVNLVPNLTVAQNLFLGYEPRRLG 110
           E      P+       F  P D +  G+     V + V+L P+LT+A        P   G
Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSL-PSLTLA--------PFGNG 384

Query: 111 LIHFKKMYAD-ARAVLTQFKLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPT 168
            +  ++   D  R +  Q  L    +   +  +S   QQ + +A+      +V   DEPT
Sbjct: 385 ALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPT 444

Query: 169 ASLDAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP 228
             +D      ++  +  L   G  I+ I+  L +V  +S+R  V   G+   E    E+ 
Sbjct: 445 VGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGDEIT 504

Query: 229 QPKLIEAMLGR 239
           + K++     R
Sbjct: 505 EEKVLSHFFER 515


Lambda     K      H
   0.319    0.136    0.377 

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: 582
Number of extensions: 30
Number of successful extensions: 7
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: 499
Length of database: 518
Length adjustment: 34
Effective length of query: 465
Effective length of database: 484
Effective search space:   225060
Effective search space used:   225060
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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