GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylGsa in Pedobacter sp. GW460-11-11-14-LB5

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS10520 CA265_RS10520 ABC
           transporter ATP-binding protein
          Length = 568

 Score =  110 bits (274), Expect = 8e-29
 Identities = 70/213 (32%), Positives = 120/213 (56%), Gaps = 6/213 (2%)

Query: 12  KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71
           K+   VKA+D ++ E+  GE + L+G++G GK+TL + I    +P  G+++F G+ +   
Sbjct: 328 KTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENITHI 387

Query: 72  SPNDARSL--GIETIYQD--LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDS 127
                R L   I+ I+QD   +L P L I  +I    +V +K++ N  +  ++  +LLD 
Sbjct: 388 GKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQV-HKLYRNDSERKQKVLELLDK 446

Query: 128 LQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNL 187
           + ++    N      SGGQRQ V +ARA+    K I+ DE  +AL V    +VL L ++L
Sbjct: 447 VGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDL 506

Query: 188 KKK-GLGVLIITHNIIQGYEVADRIYVLDRGKI 219
           + + GL  + I+H++     ++DRI V+++GKI
Sbjct: 507 QSEFGLTYIFISHDLAVVKHISDRILVMNKGKI 539



 Score = 84.3 bits (207), Expect = 5e-21
 Identities = 63/219 (28%), Positives = 114/219 (52%), Gaps = 22/219 (10%)

Query: 18  KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDR----GDLVFEGKKVIFNSP 73
           KA+  +S ++ KG V+ ++G++G+GKS     I   H        G++ FE   ++  S 
Sbjct: 21  KAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSS 80

Query: 74  NDARSLG---IETIYQD--LALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK----L 124
           N+ R +    I  I+Q+   +L P     Y      +V   I L++K    E+KK    L
Sbjct: 81  NEIRQIRGNQISMIFQEPMTSLNPVFTCGY------QVAEAIMLHRKVDQAEAKKHTIAL 134

Query: 125 LDSLQIRIPD--INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182
            + +Q+  P+         +SGGQ+Q V +A A+    K+++ DEPT AL V   + +L+
Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194

Query: 183 LARNLK-KKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
           L   LK ++ + ++ I+H++    E+AD + V+ +G+I+
Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIV 233


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: 282
Number of extensions: 16
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: 568
Length adjustment: 30
Effective length of query: 221
Effective length of database: 538
Effective search space:   118898
Effective search space used:   118898
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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