GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Bacillus altitudinis 41KF2b

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_008347408.1 BA79_RS16380 amino acid permease

Query= TCDB::P15993
         (457 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  369 bits (946), Expect = e-106
 Identities = 184/444 (41%), Positives = 276/444 (62%), Gaps = 5/444 (1%)

Query: 9   EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68
           ++LKR L NRH+QLIA+GG IGTGLFLGS   IQ AGP II  Y I G   F +MR LGE
Sbjct: 4   QELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALGE 63

Query: 69  MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128
           +++ +    S +  A  Y G +A F +GW YW  +++ AMA++ AVG Y+Q+W+ +IP W
Sbjct: 64  LLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIPQW 122

Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG---NGGPQAT 185
           + A +  +++   NL  VK+FGEMEFWFA+IKVI ++ +I  G  LL  G   + GP  T
Sbjct: 123 IPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP-VT 181

Query: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245
           V+NLW  GG  P+G TG ++   +++F++ G+ELVG++AAE  NP+++IP A N++  RI
Sbjct: 182 VTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLRI 241

Query: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305
           L FY+G++ VLL + PWT ++A  SPFV  F  +G    A  +N VVLT+A S  NS ++
Sbjct: 242 LFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGMF 301

Query: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365
             SR+L+ L+ Q   P +   ++K  VP N + VS +V ++  L++ L PE AFG++  +
Sbjct: 302 STSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTTI 361

Query: 366 VVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTPG 425
                +  W++I + H+K+++ + E    + F A   P  N   L+  AA+LVIML    
Sbjct: 362 SAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLFADA 421

Query: 426 MAISVYLIPVWLIVLGIGYLFKEK 449
              ++ L PVW   L + Y  K++
Sbjct: 422 TRPALLLTPVWFGFLFLIYARKKR 445


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: 591
Number of extensions: 26
Number of successful extensions: 3
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: 448
Length adjustment: 33
Effective length of query: 424
Effective length of database: 415
Effective search space:   175960
Effective search space used:   175960
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