GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Williamsia sterculiae CPCC 203464

Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_143690237.1 BW971_RS07675 amino acid permease

Query= TCDB::Q46065
         (463 letters)



>NCBI__GCF_900156495.1:WP_143690237.1
          Length = 480

 Score =  333 bits (855), Expect = 6e-96
 Identities = 174/432 (40%), Positives = 259/432 (59%), Gaps = 7/432 (1%)

Query: 1   MAKSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVM 60
           +A S+  LG GLR RH+ ++ LG  IGAGLF+G+GV I  AGPA +++++I G I +L+M
Sbjct: 6   VAASDAELGKGLRRRHMNLIALGGVIGAGLFVGSGVVIADAGPAAVVSFLIGGLITMLIM 65

Query: 61  QMLGEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFG 120
           +ML EMA A+P  GSF  Y   A G   GF  GWLYW+  ++V+  E      I+  W  
Sbjct: 66  RMLAEMAVAQPVVGSFYVYARRALGRRGGFVTGWLYWYFFVVVVAVEAVAGGRIVQLWLP 125

Query: 121 VEP-WIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGST 179
             P W+ SLV ++     NLV+ R FGEFEYWF+ IKV  I+ FL +GI  I G  P ST
Sbjct: 126 EVPLWVLSLVLMLTLTATNLVSARSFGEFEYWFSSIKVVAIVVFLFVGILWITGLWPDST 185

Query: 180 FVGTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVI 239
             G SN +   GF P+G   V A ++     + G EIVTIAAAESD+P +A+S A+R++I
Sbjct: 186 -PGLSNLVDHGGFTPSGWGAVLAAVVPCVAFYTGAEIVTIAAAESDEPEQAVSRAMRSII 244

Query: 240 WRISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLS 299
            RI +FY+GS+LV+  + P+ +     +   SP+  +L++  IP     M  I++ A+LS
Sbjct: 245 LRIILFYVGSILVVVTVQPWNT----KSVGVSPYASVLSVLGIPAVSTIMNLIVLTAVLS 300

Query: 300 AFNAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGL 359
             N+ +Y TSR+VF++    D PR F++LS + VP  A+LL     +VSV   Y     +
Sbjct: 301 CLNSALYTTSRMVFALTTHGDGPRFFTRLSANGVPRRAILLGTVVGYVSVAATYIWGDVV 360

Query: 360 LDFLLNAVGGCLIVVWAMITLSQLKLRKELQANDEIS-TVRMWAHPWLGILTLVLLAGLV 418
            DFL+N+ G   + V+ +I +SQ+ LR+ ++  D  +  ++MW  PWL   T+ ++  ++
Sbjct: 361 FDFLVNSYGAVALFVYLIIAVSQVVLRRRVERQDPTALRLKMWLFPWLSYATIAVMVAVI 420

Query: 419 ALMLGDAASRSQ 430
             M    ++RSQ
Sbjct: 421 LAMAFLPSTRSQ 432


Lambda     K      H
   0.327    0.140    0.428 

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: 533
Number of extensions: 31
Number of successful extensions: 6
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: 463
Length of database: 480
Length adjustment: 33
Effective length of query: 430
Effective length of database: 447
Effective search space:   192210
Effective search space used:   192210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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