GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Corynebacterium deserti GIMN1.010

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate WP_053545274.1 CDES_RS09325 amino acid permease

Query= TCDB::P15993
         (457 letters)



>NCBI__GCF_001277995.1:WP_053545274.1
          Length = 473

 Score =  330 bits (846), Expect = 6e-95
 Identities = 165/415 (39%), Positives = 265/415 (63%), Gaps = 8/415 (1%)

Query: 12  KRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGEMVV 71
           ++ LK RHIQ+IALGGA+GTGLFLG+   + + GPG+ + YA+ G I ++++R LGEMVV
Sbjct: 16  RKDLKTRHIQMIALGGALGTGLFLGAGGRLNAGGPGLAIVYAVCGLIGYMMLRSLGEMVV 75

Query: 72  EEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW--YPEIPTWV 129
             P +GSF+ ++ ++ G  A F +GW Y++ +V V +AELTA+  Y+QFW  + ++P WV
Sbjct: 76  HRPTSGSFTSYSREFLGEKAAFFAGWVYFIAWVTVGIAELTAIAVYLQFWPIFQDVPQWV 135

Query: 130 SAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGN--GGPQATVS 187
             A+   ++  +NL  VK+FGE EFWFA IKV A++  +  G +++ SG    G      
Sbjct: 136 LVALALSIVVGVNLLGVKLFGEAEFWFAFIKVAAILVFMGIGIFVIISGRDVAGHNPGFG 195

Query: 188 NLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILI 247
            L + G F P+G   L+++   ++F++ G++++G+ A E  NPE+ IP+A N  ++RI+ 
Sbjct: 196 TLHEDGWF-PNGVMPLIVLTQGVVFAYAGIDMIGVAAGETQNPEKEIPRAINTTVFRIIF 254

Query: 248 FYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYCN 307
           FY+GS+ +L  L+P +   A  SPFV   + LG    A+ +N+VVLTAALS  N+ +Y  
Sbjct: 255 FYVGSVLLLALLLPASEYKAGESPFVTFLNALGVPGAADIMNLVVLTAALSSVNAGLYAT 314

Query: 308 SRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALVV 367
           +R+L  LA  G+APK L  + K GVP+  + ++  +  L V++NY+ P  AF +++    
Sbjct: 315 ARVLKPLAHTGSAPKFLGVMSKHGVPMGGVWLTTALLILGVILNYVVPSQAFEIVLNFGA 374

Query: 368 SALVINWAMISLAHMKFRRAKQEQGVVTR--FPALLYPLGNWICLLFMAAVLVIM 420
            A++  W MI +AH+ + +A +E G VTR  + A L   G+WI ++F+  V+V+M
Sbjct: 375 IAILAMWTMIVVAHLGYLKAAKE-GKVTRHSYRAPLGAAGDWIVIIFLVGVVVLM 428


Lambda     K      H
   0.328    0.141    0.434 

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: 587
Number of extensions: 30
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: 457
Length of database: 473
Length adjustment: 33
Effective length of query: 424
Effective length of database: 440
Effective search space:   186560
Effective search space used:   186560
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