GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Kocuria flava HO-9041

Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_083529130.1 AS188_RS01250 amino acid permease

Query= TCDB::Q46065
         (463 letters)



>NCBI__GCF_001482365.1:WP_083529130.1
          Length = 482

 Score =  378 bits (970), Expect = e-109
 Identities = 199/438 (45%), Positives = 282/438 (64%), Gaps = 6/438 (1%)

Query: 9   GTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMAA 68
           G  L+ RHL MM LGSAIG GLF+G+G  +R AGPAVLL++++A  ++VLVM+ LGEMAA
Sbjct: 23  GARLKARHLVMMALGSAIGTGLFIGSGAAVRTAGPAVLLSFLVACVLLVLVMRALGEMAA 82

Query: 69  ARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGA-WFGVEPWIPS 127
           A P+ G+FS + E+A G   G +LGWL+W  +++V+ AE T AA ++   W   E W+ +
Sbjct: 83  ADPSPGAFSTWAENAMGRTVGRTLGWLWWAQIVVVVAAEATAAAQLLTELWPVTEQWVLA 142

Query: 128 LVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFI 187
           LV +V F V+NLV VR  GE E+WFA +KV  ++ FL +G+AL+ G L   +  G  N  
Sbjct: 143 LVFMVVFTVINLVKVRTLGETEFWFALMKVLAVLVFLAVGVALLLGLLEVPS-PGLRNLT 201

Query: 188 GDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYL 247
              GF+P G++GVAA LL V FAFGG E+VTIAAAE++ P+  ++ A+R ++ RI VFY+
Sbjct: 202 AHGGFLPTGLTGVAAALLVVIFAFGGTELVTIAAAETEDPQHNVARAIRTILVRILVFYV 261

Query: 248 GSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYA 307
           G+V V+  ++P+      +  + SPF  +L  A +PG    M  II+LALLSA NA IY 
Sbjct: 262 GAVTVMVLVLPWND----EQLSVSPFVAVLEAAGVPGADVVMAVIIILALLSALNANIYG 317

Query: 308 TSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAV 367
           +SR+++S+A R  APR F+ LS   VP  AV++S+ F F +V L Y  P  +L ++LN V
Sbjct: 318 SSRMLYSLARRGSAPRAFADLSDRGVPRTAVVVSVVFGFAAVVLNYLWPETVLLWMLNTV 377

Query: 368 GGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAAS 427
           G   +VVW +  +SQ+ LR+       +  +RMWA PWL    L LLAG+V L L D A 
Sbjct: 378 GATCLVVWGLALVSQIVLRRRADRAGTVLPLRMWAFPWLSWFALALLAGIVLLGLLDDAV 437

Query: 428 RSQVYSVAIVYGFLVLLS 445
           R Q+   A +   + LL+
Sbjct: 438 RVQLLLTAGLVALIALLA 455


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: 599
Number of extensions: 24
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: 482
Length adjustment: 33
Effective length of query: 430
Effective length of database: 449
Effective search space:   193070
Effective search space used:   193070
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