Alignments for a candidate for araVsh in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Moritella dasanensis ArB 0140

Align ABC transporter related (characterized, see rationale)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  341 bits (875), Expect = 3e-98
 Identities = 186/491 (37%), Positives = 303/491 (61%), Gaps = 8/491 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           IL+L  I K +PGVKAL++  L ++ G+V ALLGENGAGKSTL+KV+TG    D G I +
Sbjct: 5   ILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINY 64

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRR-LGLIHFKKMYADAR 122
            G    F+ P  +Q+ GIS ++QE+NL+P LT+A+N++LG E     G I + +M+ADA 
Sbjct: 65  QGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNAFGGIKWTQMFADAD 124

Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
           A+L +  +       L + S+  QQ++ IA+ ++  ++V+V+DEPT +L   E + LF +
Sbjct: 125 ALLQRLNVKHSSRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFKV 184

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           +N+L+ +G  IV+I+H L ++++I D ITVLR+G+FI E    ++ +  LIE M+GR L 
Sbjct: 185 INELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMVGRRLD 244

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
           E       K  T+       L +E++   G ++ ++ T+  G+ +G++GL+G+GR+E+  
Sbjct: 245 EIYPRIDAKHGTLC------LEVENIVAPG-VRDVSFTLDHGEILGISGLMGAGRTELMK 297

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362
           A++G     SG + L  + ++   P D ++ GIA   EDRK DG+I  LS++EN+ L   
Sbjct: 298 AIYGALPRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSLCAL 357

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
             +     L + ++    + F+ +  + TP  D+ I  LSGGNQQKV +A+ L   P +L
Sbjct: 358 DALSKGLQLDHAKEATAVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVL 417

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482
           +LDEPTRG+D+GA  EI +LI     EGMS+++ SSE+ E++  S++++V+ +     E 
Sbjct: 418 ILDEPTRGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEGRISGEF 477

Query: 483 SGAELTSQHVM 493
             A+   + +M
Sbjct: 478 MAADANQEKLM 488



 Score =  110 bits (276), Expect = 9e-29
 Identities = 79/256 (30%), Positives = 135/256 (52%), Gaps = 21/256 (8%)

Query: 2   SLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61
           +L LE++ I    PGV+   DVS  L  GE+  + G  GAG++ L+K + GA  +  GD+
Sbjct: 256 TLCLEVENIVA--PGVR---DVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDV 310

Query: 62  LFLGEPQHFNTPMDAQKAGISTVYQEVN---LVPNLTVAQNLFL---GYEPRRLGLIHFK 115
           +   +     TP D    GI+ + ++     L+  L+V +N+ L       + L L H K
Sbjct: 311 ILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSLCALDALSKGLQLDHAK 370

Query: 116 KMYADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTAS 170
           +  A     +  F    +V  P  D  I       QQ +AIA+G+    KVL+LDEPT  
Sbjct: 371 EATA-----VEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRG 425

Query: 171 LDAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQP 230
           +D    + ++ ++NQ KA+G++I+ ++  + +V  +SDRI V+  G+  GE++ A+  Q 
Sbjct: 426 VDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQE 485

Query: 231 KLIEAMLGRSLQEQLV 246
           KL+   +G+ + E ++
Sbjct: 486 KLMACAVGKKINEAVL 501



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 54/221 (24%), Positives = 106/221 (47%), Gaps = 15/221 (6%)

Query: 279 LTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALC 338
           L V  G+ + L G  G+G+S +   + G+  +D GSI+  G  +    P  +   GI++ 
Sbjct: 26  LNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINYQGSDVTFDGPRHSQEVGISII 85

Query: 339 PEDRKIDGIIGPLSIRENIILALQAR-----IGWWRYLSNTRQQEIAQFFIDKLQIATPD 393
            ++  +   I  L+I ENI L  +       I W +  ++      A   + +L +    
Sbjct: 86  HQELNL---IPELTIAENIYLGRETTNAFGGIKWTQMFAD------ADALLQRLNVKH-S 135

Query: 394 ADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSL 453
           + + + +LS G QQ V +A+ L+ +  ++V+DEPT  +       + K+I  L +EG  +
Sbjct: 136 SRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFKVINELRNEGCGI 195

Query: 454 LVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494
           +  S  L E+    + + VLRD   + E++  ++    +++
Sbjct: 196 VYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIE 236


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: 590
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 501
Length adjustment: 34
Effective length of query: 465
Effective length of database: 467
Effective search space:   217155
Effective search space used:   217155
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources