GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Oleispira antarctica RB-8

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_046008336.1 OLEAN_RS05080 ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_000967895.1:WP_046008336.1
          Length = 303

 Score =  102 bits (255), Expect = 1e-26
 Identities = 70/215 (32%), Positives = 118/215 (54%), Gaps = 11/215 (5%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           L+E +N+TK +    A+NN++ +I  G+  ALVG NGAGKSTL  ILAG  P   G+  +
Sbjct: 4   LIECQNLTKAYGNKKALNNISFEIQSGQPIALVGPNGAGKSTLFGILAGYIPATSGEAKI 63

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENI-FLSREPVNEFGVIEYQKMFEQA 130
            G  V   +P       I  +PQ+    PNL+  + + FL+R  +  FG     K F++A
Sbjct: 64  LGHNV--GSPELI--GRIGALPQDALFNPNLTIQQQLSFLAR--LQGFG---RSKAFKEA 114

Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190
           +++   + +    K K+  LS   ++ VAIA+AL  + +++++DEPT+ +       +  
Sbjct: 115 ARVLELMQLADTAKEKITALSHGMKKRVAIAQALMGEPELVLLDEPTAGLDPENARNIRQ 174

Query: 191 IIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDG 225
            + +L +E   VI  SH LEE+  + ++V+ +  G
Sbjct: 175 QVMALSDETTFVI-SSHNLEELERLCEQVLYLDQG 208



 Score = 62.4 bits (150), Expect = 2e-14
 Identities = 63/241 (26%), Positives = 115/241 (47%), Gaps = 22/241 (9%)

Query: 280 KLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRD 339
           K  ++++SF ++ G+ + + G  GAG++ L   + G  P  T G+  I G  +   SP  
Sbjct: 17  KKALNNISFEIQSGQPIALVGPNGAGKSTLFGILAGYIPA-TSGEAKILGHNVG--SPE- 72

Query: 340 AVKNGIGLVPEDRK-TAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIE 398
            +   IG +P+D      L +Q             +  + R  G   S+  KE  R  +E
Sbjct: 73  -LIGRIGALPQDALFNPNLTIQQQ-----------LSFLARLQGFGRSKAFKEAAR-VLE 119

Query: 399 KLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISE 458
            + +   +  +I   LS G +++V +A+ L  +P+++LLDEPT G+D      I + +  
Sbjct: 120 LMQLADTAKEKITA-LSHGMKKRVAIAQALMGEPELVLLDEPTAGLDPENARNIRQQV-- 176

Query: 459 MAVSGMGVVMVSS-ELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVE 517
           MA+S     ++SS  L E+  + +++L + +G   A+ +  + TE+  L     R V   
Sbjct: 177 MALSDETTFVISSHNLEELERLCEQVLYLDQGELKAQHIIGQQTEQQTLSYLTVRLVVKN 236

Query: 518 T 518
           T
Sbjct: 237 T 237


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: 314
Number of extensions: 21
Number of successful extensions: 4
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: 303
Length adjustment: 31
Effective length of query: 492
Effective length of database: 272
Effective search space:   133824
Effective search space used:   133824
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 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