GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Acidovorax sp. GW101-3H11

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Ac3H11_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_694
          Length = 341

 Score =  192 bits (487), Expect = 1e-53
 Identities = 111/320 (34%), Positives = 181/320 (56%), Gaps = 9/320 (2%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           LL+  ++R ++      V+AVD +SF I   E +G+VGESG GK+T+  ++   +V P +
Sbjct: 20  LLEIAHLRKHFGSGPHPVRAVDDVSFTIHRGETLGLVGESGSGKSTIGRLL-TRLVDPTS 78

Query: 65  LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124
              G++         +L+ +++ + +      +I II Q    +L P +R+   +    +
Sbjct: 79  ---GQMRYHGGAAPQDLAQLSQSQYRPL--RSQIQIIFQDPYASLNPRMRIRDVLAEALD 133

Query: 125 SHGIDEEEL-LDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADE 183
           +HG+ +    L +  +  E+VGL P   +R+P E SGG RQR  IA A  + P  ++ADE
Sbjct: 134 THGLAKGAARLPRIHQLLEQVGLRPEHAERFPHEFSGGQRQRIGIARALAVEPQFIVADE 193

Query: 184 PTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPV 243
           P SALDV  Q  ++ +L ++K Q +  +++FI+HD+  V  + DR++++Y G+++E AP 
Sbjct: 194 PLSALDVSIQAQVVNLLGELKEQ-LGLTLLFISHDLDVVEYLCDRVVVLYLGRVMEIAPT 252

Query: 244 ESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDV 303
           E+L  +P HPYTQ L  +   P+P  ++R I  + G  P+  NPPSGC F  RCP A   
Sbjct: 253 EALYAQPQHPYTQALLAAAPIPDP-AQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEAR 311

Query: 304 CKEKEPPLTEIEPGRRVACW 323
           C   +  L E+ PG   ACW
Sbjct: 312 CASADMQLREVAPGHLHACW 331


Lambda     K      H
   0.321    0.138    0.405 

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: 270
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 330
Length of database: 341
Length adjustment: 28
Effective length of query: 302
Effective length of database: 313
Effective search space:    94526
Effective search space used:    94526
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 (21.8 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