GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Planococcus halocryophilus Or1

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_000342445.1:WP_008497300.1
          Length = 310

 Score =  113 bits (283), Expect = 9e-30
 Identities = 72/226 (31%), Positives = 126/226 (55%), Gaps = 9/226 (3%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           +L+   +TK F   +AV+ VT+++ +GE   L+G NGAGKST + +++ +     G + L
Sbjct: 1   MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENI-FLSREPVNEFGVIEYQKMFEQA 130
            GK V  + P E ++  + ++PQ++ L   LS+ EN+ F  R     +G +  +K+ E+ 
Sbjct: 61  NGKSV-LKKPGEMRK-VLGVVPQKIALYEELSAYENLKFFGR----IYG-LSGKKLEERI 113

Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190
             +   +G++   K  V+  S   Q+ V +A A+  + +++IMDEPT  I  +    L  
Sbjct: 114 QIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGIDPQSRNHLLE 173

Query: 191 IIRSLKNE-GKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEE 235
            IR L  E G +V+Y SH +EE+ ++ DRV +M  G+ +  G  +E
Sbjct: 174 TIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDE 219



 Score = 80.9 bits (198), Expect = 6e-20
 Identities = 64/230 (27%), Positives = 119/230 (51%), Gaps = 16/230 (6%)

Query: 272 KLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKE 331
           KL    +  L VD+V+  + +GE +G+ G  GAG++  +  I       T G V + GK 
Sbjct: 6   KLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMI-STLIQPTSGDVRLNGKS 64

Query: 332 IKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKE 391
           + +  P + ++  +G+VP+      L  ++S   N+       K   R +GL   +LE+ 
Sbjct: 65  V-LKKPGE-MRKVLGVVPQK---IALYEELSAYENL-------KFFGRIYGLSGKKLEER 112

Query: 392 IVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSE 451
           I    + +L   +    ++V+  SGG Q++V LA  +  +P+VL++DEPT GID  +++ 
Sbjct: 113 I--QIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGIDPQSRNH 170

Query: 452 IYKLISEM-AVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEV 500
           + + I ++    GM V+  S  + E+  + DR+ +M  G+  A   ++E+
Sbjct: 171 LLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDEL 220


Lambda     K      H
   0.317    0.137    0.372 

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: 382
Number of extensions: 21
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: 523
Length of database: 310
Length adjustment: 31
Effective length of query: 492
Effective length of database: 279
Effective search space:   137268
Effective search space used:   137268
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