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_083529221.1 AS188_RS03395 amino acid permease

Query= TCDB::Q46065
         (463 letters)



>NCBI__GCF_001482365.1:WP_083529221.1
          Length = 496

 Score =  374 bits (960), Expect = e-108
 Identities = 198/434 (45%), Positives = 283/434 (65%), Gaps = 10/434 (2%)

Query: 12  LRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMAAARP 71
           L+ RHL MM LGSAIG GLF+GTG  I  AGPAVL+++++A  ++VLVM+ +GEMAAA P
Sbjct: 32  LKPRHLVMMALGSAIGTGLFVGTGSAIALAGPAVLISFLVACVVLVLVMRAMGEMAAADP 91

Query: 72  ASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEP-WIPSLVC 130
           A G+FS Y E A G  AG +LGWL+W  L++V+ AE T AA I+   + V P W  +L  
Sbjct: 92  ARGAFSVYAEKALGRTAGQTLGWLWWAQLVVVIAAEATAAAQILSELWPVLPQWSLALAF 151

Query: 131 VVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFIGDH 190
           +V F  +NLV+VR  GE E+WFA +KV  ++AFL++G AL+ G LP S   G +N     
Sbjct: 152 MVVFTALNLVSVRALGESEFWFALLKVGAVVAFLLVGAALLLGLLP-SPSPGLANLTAHG 210

Query: 191 GFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYLGSV 250
           GFMP G++GVAA LL V FAFGG E+VT+AAAE+  P+  ++ A+R ++ R+ VFY+GSV
Sbjct: 211 GFMPTGVTGVAAALLVVVFAFGGTELVTVAAAETRDPQRNVARAIRTIVVRVLVFYVGSV 270

Query: 251 LVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYATSR 310
            ++  ++P+ +    ++ + SPF  +L++A +PG    M  +I LALLSA NA +Y  SR
Sbjct: 271 ALMVLILPWNT----ESLSSSPFVAVLSVAGLPGAQAVMAVVIALALLSALNANLYGASR 326

Query: 311 LVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAVGGC 370
           ++ S+++R  APR F +LS S VP  AV+ S+ F FV+V L Y  P  +L FLLN +G  
Sbjct: 327 MLHSLSDRGCAPRRFVRLSGSGVPVPAVVASVLFGFVAVVLNYLWPEAVLGFLLNTIGST 386

Query: 371 LIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAASRSQ 430
           ++VVWA+  +SQ+ LR+          +RMW  P+L  L L L+ G++ L   D   R+Q
Sbjct: 387 VLVVWALSLVSQIVLRRRADREGRELPLRMWGFPYLSWLALALVGGILVLGWFDPVVRTQ 446

Query: 431 VYSVAIVYGFLVLL 444
           +    ++ G LV L
Sbjct: 447 L----VLTGGLVAL 456


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: 631
Number of extensions: 32
Number of successful extensions: 4
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: 496
Length adjustment: 34
Effective length of query: 429
Effective length of database: 462
Effective search space:   198198
Effective search space used:   198198
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