GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_013402865.1 CALHY_RS04750 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>NCBI__GCF_000166355.1:WP_013402865.1
          Length = 370

 Score =  138 bits (348), Expect = 1e-37
 Identities = 76/211 (36%), Positives = 120/211 (56%), Gaps = 7/211 (3%)

Query: 1   MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60
           M+SV ++ V + +         A+   + ++ D +F+ ++GPSGCGK+T LR++AGL+  
Sbjct: 1   MASVRLKGVYKRYPGG----VTAVSDFNLDIEDKEFIVLVGPSGCGKTTTLRMIAGLEEV 56

Query: 61  TSGRVLLDGAPVEG-PGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAA 117
           T G + +    V   P  +R   MVFQ+Y L+P +T+ +N+ FGL+ R  P+ + K R  
Sbjct: 57  TEGEIYIGDKLVNDVPPKDRDIAMVFQNYALYPHMTVFENMAFGLKLRKFPKDEIKRRVH 116

Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177
                +G+       PK LSGG +QR A+ RA+  +PK+ LMDEP   LD + RV M+  
Sbjct: 117 EAAKILGIEHLLDRKPKALSGGQRQRVALGRAIVREPKVFLMDEPLSNLDAKLRVQMRTE 176

Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAV 208
           L  + +    T ++VTHD  EA+ M  R+ V
Sbjct: 177 LSKLHKRLGTTFIYVTHDQTEAMTMGTRIVV 207


Lambda     K      H
   0.322    0.136    0.394 

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: 208
Number of extensions: 8
Number of successful extensions: 2
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: 259
Length of database: 370
Length adjustment: 27
Effective length of query: 232
Effective length of database: 343
Effective search space:    79576
Effective search space used:    79576
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 (21.9 bits)
S2: 48 (23.1 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