GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Shewanella loihica PV-4

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)

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



>FitnessBrowser__PV4:5210215
          Length = 227

 Score =  141 bits (355), Expect = 1e-38
 Identities = 76/216 (35%), Positives = 124/216 (57%), Gaps = 10/216 (4%)

Query: 3   SVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATS 62
           +++IQA+++++         A++ +D  +   +FV I+GPSG GK+TLL ++ G+D  +S
Sbjct: 2   TIAIQALTKIYNPESDFPVAAVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSS 61

Query: 63  GRVLLDGAPVEGPGAER---------GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK 113
           G V +DG  +     +          G +FQ Y+L P LT  +N+ F ++ +G  EA+ +
Sbjct: 62  GAVFIDGEDITHLSEQALIAFRRDHVGFIFQDYSLLPVLTALENVEFVMQLQGHSEAECR 121

Query: 114 ERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVL 173
           +RA   +A+VGL   +   P +LSGG QQR A+ARALA  P+ ++ DEP   LD ++   
Sbjct: 122 DRAMALLAQVGLAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAE 181

Query: 174 MQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVF 209
           + +++  + E E  T +F THD    I  A RV VF
Sbjct: 182 LLDIMQSLNEQEGTTFIFSTHD-PRVIARAKRVIVF 216


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: 136
Number of extensions: 7
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: 227
Length adjustment: 23
Effective length of query: 236
Effective length of database: 204
Effective search space:    48144
Effective search space used:    48144
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: 46 (22.3 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