GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Acidovorax sp. GW101-3H11

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  142 bits (359), Expect = 1e-38
 Identities = 80/238 (33%), Positives = 133/238 (55%), Gaps = 2/238 (0%)

Query: 1   MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60
           MS  +E R+V K FG V+ L GV   +  G V  LLG+NGAGKSTL+KI++GY  P  G+
Sbjct: 1   MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60

Query: 61  LVFEGK-KVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMME 119
           +V +G  +        A + GI  I+Q+  L  DL I  NIFL  E+   +FL+ K M E
Sbjct: 61  VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMRE 120

Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179
           ++++ L  + + + D + +V  L   ++Q V +ARA+  +A++++MDEPTA L+  E  +
Sbjct: 121 KTREALAKVGLPL-DPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179

Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
           +  L   LK  G+ ++ I+H + +     D + V+  G ++  +        ++  +M
Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLM 237



 Score = 84.7 bits (208), Expect = 3e-21
 Identities = 53/222 (23%), Positives = 109/222 (49%), Gaps = 14/222 (6%)

Query: 21  DGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLG 80
           +GV  E+ +GE++   G  GAG++ L + + G      G +   G+ V   SP DA   G
Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331

Query: 81  IETIYQD---------LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDSLQIR 131
           +  + +D           L P+L +     +A E   K +L+        ++ +    IR
Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTL-----MALERYAKPWLDPAAEQAALREAVQEFGIR 386

Query: 132 IPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKG 191
              + ++  +LSGG +Q +A+A+ ++    ++++DEPT  + V   R++  L + L ++G
Sbjct: 387 TGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQG 446

Query: 192 LGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
           L V++I+  +++   +  R+ V+  G++    ++     EE+
Sbjct: 447 LAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEEL 488


Lambda     K      H
   0.318    0.137    0.371 

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: 227
Number of extensions: 12
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: 251
Length of database: 496
Length adjustment: 29
Effective length of query: 222
Effective length of database: 467
Effective search space:   103674
Effective search space used:   103674
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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