GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Phaeobacter inhibens BS107

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate GFF3834 PGA1_262p02380 putative histidine transport system permease protein HisM

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__Phaeo:GFF3834
          Length = 258

 Score =  152 bits (383), Expect = 8e-42
 Identities = 88/223 (39%), Positives = 127/223 (56%), Gaps = 10/223 (4%)

Query: 4   WELILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRG 63
           W+ I  + P  L+G   T+ +L +  + G ALA+PLG+A+A   WY+      +    RG
Sbjct: 32  WDWIPTYAPLALEGLWTTIWILVVTSILGFALAVPLGLAQAVGPWYLSTPARIFCTVIRG 91

Query: 64  TPLLLQLFIVYYGLA----QFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAI 119
           TPLLLQ++++YYGL     QF  +R S  WPYLR  +  A+L +TL  A Y  E++RGA 
Sbjct: 92  TPLLLQIWLLYYGLGSLFPQFPWIRSSELWPYLRQAWPYAVLALTLSYAGYEGEVMRGAF 151

Query: 120 HSVPVGEVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDI 179
             V  G++EAA+A GM R      I LP+AVR  LP    E IL LKA+ +V T+T+ DI
Sbjct: 152 SGVAKGQLEAAKAYGMPRLTMFRRIWLPQAVRNVLPTLGGETILQLKATPLVATITVLDI 211

Query: 180 MGMARTIIART---YESMLFFCLAGALYLVITIVLTRIFRLIE 219
             ++  + + T   YE +L   L   +Y+ I  V+T  F+  E
Sbjct: 212 YAVSSRVRSDTFIVYEPLLLLAL---VYMAIAGVITLAFKRFE 251


Lambda     K      H
   0.332    0.142    0.443 

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: 178
Number of extensions: 14
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: 230
Length of database: 258
Length adjustment: 24
Effective length of query: 206
Effective length of database: 234
Effective search space:    48204
Effective search space used:    48204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 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