GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Desulfotomaculum hydrothermale Lam5

Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate WP_008411161.1 DESHY_RS05820 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TZ92
         (517 letters)



>NCBI__GCF_000315365.1:WP_008411161.1
          Length = 280

 Score =  109 bits (272), Expect = 1e-28
 Identities = 83/254 (32%), Positives = 127/254 (50%), Gaps = 8/254 (3%)

Query: 27  ITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQFNGQDFRPGSRTQAEELGVR 86
           ++L +  GE   L G NGAGK+T  +++  L  PT G +  NGQ     +     ++G  
Sbjct: 20  LSLHIKPGEFFGLLGPNGAGKTTTLRLLTALTPPTAGQITVNGQPVSRNNTAAKRQIG-- 77

Query: 87  MVMQELNLLPTLTVAENLFLDNLPSHCGWISRKQLRKAAIEAMAQVGLDAIDPDTLVGSL 146
           +V Q +NL P LTV ENL L  L  +   +SR+++ +     +A   L A +   L G+L
Sbjct: 78  LVPQHINLEPELTVEENLRLHGLLYN---MSRQEINRRIDRLLAFSDL-AAERKALAGNL 133

Query: 147 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISHRLE 206
             G ++ V IAR L+    +L+LDEPTA L       +++ I  L ARG+ I+  +H LE
Sbjct: 134 SGGMKRKVMIARALMHQPALLLLDEPTAGLDVFSRRRVWDLIKSLNARGMTILLTTHYLE 193

Query: 207 ELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTLMVGRELGEHIDLGPRTIGGPALT-VK 265
           E   +  RI +L+ G+L+    +     +Q+  ++V    G   DL      G AL    
Sbjct: 194 EAEHLCSRIGLLKKGRLIMTGSVEELR-QQVGPVVVEVFAGHQTDLYFFRDQGSALDFAA 252

Query: 266 GLTRSDKVRDVSFE 279
           GLT    +R  S E
Sbjct: 253 GLTNEFTIRQASLE 266



 Score = 84.0 bits (206), Expect = 6e-21
 Identities = 68/232 (29%), Positives = 111/232 (47%), Gaps = 15/232 (6%)

Query: 273 VRDVSFEVRAGEIYGISGLIGAGRTELLRLIFGADLADSGTVALGSPAQVVSIRSPVDAV 332
           V  +S  ++ GE +G+ G  GAG+T  LRL+       +G + +    Q VS  +   A 
Sbjct: 17  VDHLSLHIKPGEFFGLLGPNGAGKTTTLRLLTALTPPTAGQITVNG--QPVSRNNT--AA 72

Query: 333 GHGIALITEDRKGEGLLLTQSISANIALGNMPEISGGGVVNSRDETALAKRQIDAMRIRS 392
              I L+ +    E  L   ++  N+ L  +        +N R +  LA   + A R   
Sbjct: 73  KRQIGLVPQHINLEPEL---TVEENLRLHGLLYNMSRQEINRRIDRLLAFSDLAAER--- 126

Query: 393 SSPAQLVSELSGGNQQKVVIGRWLERDCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGK 452
                L   LSGG ++KV+I R L    +++L DEPT G+DV ++  ++ L+  L  +G 
Sbjct: 127 ---KALAGNLSGGMKRKVMIARALMHQPALLLLDEPTAGLDVFSRRRVWDLIKSLNARGM 183

Query: 453 ALVVVSSDLRELMLICDRIGVLSAGRLIETFERDSWTQD--ELLAAAFAGYQ 502
            +++ +  L E   +C RIG+L  GRLI T   +   Q    ++   FAG+Q
Sbjct: 184 TILLTTHYLEEAEHLCSRIGLLKKGRLIMTGSVEELRQQVGPVVVEVFAGHQ 235


Lambda     K      H
   0.319    0.136    0.382 

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: 318
Number of extensions: 19
Number of successful extensions: 5
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: 517
Length of database: 280
Length adjustment: 30
Effective length of query: 487
Effective length of database: 250
Effective search space:   121750
Effective search space used:   121750
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 (21.7 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