GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pseudovibrio axinellae Ad2

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_068000557.1 PsAD2_RS00555 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IUD1
         (522 letters)



>NCBI__GCF_001623255.1:WP_068000557.1
          Length = 522

 Score =  384 bits (986), Expect = e-111
 Identities = 207/495 (41%), Positives = 308/495 (62%), Gaps = 8/495 (1%)

Query: 14  LTLSGIGKRYAA-PVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLD 72
           L + G+ K +     LDG+   L+ G+V AL GENGAGKSTL KI+ G+    +G + L+
Sbjct: 19  LDVQGVKKYFGGVKALDGVSFSLKQGEVHALVGENGAGKSTLIKILSGVYSFDSGNISLE 78

Query: 73  GQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPR-RFGWIDRKKLAEAARA 131
              Y P S  +A+  GI++V QE NL+  LSIAEN+ +E+LPR ++G +++ ++   AR 
Sbjct: 79  NTSYQPESPQEAKARGIQVVHQEFNLLEHLSIAENISIERLPRNKYGLLNKGEMNRRARE 138

Query: 132 QMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSR 191
            ++ +GL ++D   PVG LG+ H+Q++EIAR L    + LILDEPTA LT RE + LF  
Sbjct: 139 ALDAIGLTDIDVRVPVGSLGIAHRQLIEIARALQSKSQILILDEPTATLTERETKRLFKI 198

Query: 192 IERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGELTK 251
           I  +++EGV ++++SH L+E+  I DR+ V R+GK V  D I   + E +VQ M G   +
Sbjct: 199 IAAIKSEGVTVVFVSHHLDEVFAICDRVTVFRNGKTVATDKISHMTPEGVVQRMVGRHLE 258

Query: 252 VDL--DAEHRRIGAPVLRIRGLGRAPVVHPA--SLALHAGEVLGIAGLIGSGRTELLRLI 307
                  + +  G   L+I  +           SL LH GE++GIAGL+GSGR+E+LR I
Sbjct: 259 AGTRQHTDKQTFGPVALQIDAMRTMQNTGDTGISLNLHYGEIVGIAGLVGSGRSEILRGI 318

Query: 308 FGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANL 367
           FG D    G ++     E    + P+DA+KAGI  VTEDRK +GL+L   I+ NTSL N+
Sbjct: 319 FGIDPIHSGTVY--RDGEEVNFKGPQDAIKAGIGFVTEDRKDEGLILDMPIAANTSLVNI 376

Query: 368 GSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIM 427
             +S+ G++    E+  A++   +L+++ G  A  A  LSGGNQQKVV+A+WL  +  ++
Sbjct: 377 HELSKTGLIQFTEENRQARESGSRLKLKYGKTADPASSLSGGNQQKVVLAKWLACNPKVL 436

Query: 428 LFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTF 487
           L DEPTRG+D+GAK++IY +  +LA +G  LLVVSS++ ELM + DRI V++   I    
Sbjct: 437 LLDEPTRGVDVGAKAEIYSILKDLAQEGVALLVVSSEMPELMTLADRIVVLAEHAIQGEL 496

Query: 488 SRDDWSQERILAAAF 502
              ++S+E IL  A+
Sbjct: 497 KPSEFSEENILKLAY 511



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 5/224 (2%)

Query: 30  GIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMMLDGQPYAPASRTQAEGLGI 89
           GI L+L  G+++ + G  G+G+S + + I G+    +G +  DG+         A   GI
Sbjct: 290 GISLNLHYGEIVGIAGLVGSGRSEILRGIFGIDPIHSGTVYRDGEEVNFKGPQDAIKAGI 349

Query: 90  RMVMQELN---LIPTLSIAENLFLEKLPR--RFGWIDRKKLAEAARAQMEVVGLGELDPW 144
             V ++     LI  + IA N  L  +    + G I   +    AR     + L      
Sbjct: 350 GFVTEDRKDEGLILDMPIAANTSLVNIHELSKTGLIQFTEENRQARESGSRLKLKYGKTA 409

Query: 145 TPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSRIERLRAEGVAIIY 204
            P   L  G+QQ V +A+ L  + + L+LDEPT  +       ++S ++ L  EGVA++ 
Sbjct: 410 DPASSLSGGNQQKVVLAKWLACNPKVLLLDEPTRGVDVGAKAEIYSILKDLAQEGVALLV 469

Query: 205 ISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGE 248
           +S  + EL  +ADRIVVL +  +        +S E +++L  G+
Sbjct: 470 VSSEMPELMTLADRIVVLAEHAIQGELKPSEFSEENILKLAYGQ 513


Lambda     K      H
   0.320    0.137    0.390 

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: 632
Number of extensions: 32
Number of successful extensions: 9
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: 522
Length of database: 522
Length adjustment: 35
Effective length of query: 487
Effective length of database: 487
Effective search space:   237169
Effective search space used:   237169
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 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