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_076479006.1 BW971_RS09675 amino acid permease

Query= TCDB::Q46065
         (463 letters)



>NCBI__GCF_900156495.1:WP_076479006.1
          Length = 605

 Score =  308 bits (789), Expect = 3e-88
 Identities = 165/439 (37%), Positives = 251/439 (57%), Gaps = 10/439 (2%)

Query: 8   LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67
           L   L  R L+M+ +G  IGAGLF+G+GV I   GP   + Y +AG ++++VM+ L EMA
Sbjct: 6   LNKSLSQRQLSMIAIGGVIGAGLFVGSGVVIHDTGPGTFITYALAGLLIIMVMRALAEMA 65

Query: 68  AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEP-WIP 126
            A P++GSF+ Y   A G+WAGFS+GWLYW+  ++V+G E    A I+  W    P W+ 
Sbjct: 66  VASPSTGSFADYSRRALGNWAGFSVGWLYWYFWVIVVGFEAIAGAKIVQYWIPSAPTWLT 125

Query: 127 SLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNF 186
           +++ +      NL +V  FGEFEYWFA IKVA II FL++G+  +FG  PG + +  SN 
Sbjct: 126 AMLLLAAMTATNLFSVSSFGEFEYWFASIKVAAIIVFLVLGVVFVFGLWPGKS-MDFSNL 184

Query: 187 IGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFY 246
               GF P G + +  G++ V F+  G EI TIAAAES  P  A+S A  +VI RI++FY
Sbjct: 185 TSHGGFFPKGGTAITVGVVTVIFSMVGAEIATIAAAESQDPERAVSRAANSVIARIALFY 244

Query: 247 LGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIY 306
           +GS  ++  ++P+      D+ + SPF        IP     M A+++ A+LS  N+ +Y
Sbjct: 245 VGSAFLLVTILPWND----DSVSGSPFVAAFTEMGIPAADHIMNAVVLTAVLSCLNSGMY 300

Query: 307 ATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSV-GLQYWNPAGLLDFLLN 365
             SR++F +A +++AP     ++   VP NA+L S    F+ V    +W    +  FLLN
Sbjct: 301 TGSRMLFVLAAKREAPAQLVAVTRRGVPRNAILASSVIGFLCVIAAAFWENT-IFTFLLN 359

Query: 366 AVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDA 425
           + G  ++ V+ +I +SQ  LR   ++      V+MW  P L +LT   +  ++  M  D 
Sbjct: 360 SSGAIILFVYLLIVVSQTVLR--FRSGSADLKVKMWFFPVLSLLTAAAILAILVQMGLDP 417

Query: 426 ASRSQVYSVAIVYGFLVLL 444
           A RSQ+    + +  +VLL
Sbjct: 418 AVRSQLVLSLVSWAVVVLL 436


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: 678
Number of extensions: 43
Number of successful extensions: 5
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: 605
Length adjustment: 35
Effective length of query: 428
Effective length of database: 570
Effective search space:   243960
Effective search space used:   243960
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: 52 (24.6 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