GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Burkholderia phytofirmans PsJN

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 BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15500 BPHYT_RS15500 aromatic
           amino acid transporter
          Length = 461

 Score =  654 bits (1687), Expect = 0.0
 Identities = 314/450 (69%), Positives = 369/450 (82%)

Query: 2   MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61
           M   Q  + LKRGLKNRHIQLIALGGAIGTGLFLGSASV+Q+AGP +ILGYAI G IAF+
Sbjct: 1   MNSAQQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFM 60

Query: 62  IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121
           IMRQLGEMV +EPVAGSFSHFAYKYWG F GF SGWNYWVLYVLV+MAELTAVG YI +W
Sbjct: 61  IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYW 120

Query: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGG 181
           +P +PTWVSA V F +INAINL NVK +GE EFWFAIIKV+AV+ MI+FGG+LL SG+GG
Sbjct: 121 WPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGG 180

Query: 182 PQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 241
           PQA+++NLW  GGF PHGF GL MM+A+IMFSFGGLEL+GITAAEAD P++SIPKA NQV
Sbjct: 181 PQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQV 240

Query: 242 IYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 301
           IYRILIFYI SL VLLSL PW  V A  SPFV+IF ++G T  AN LN+VVLTAALSVYN
Sbjct: 241 IYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300

Query: 302 SCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGL 361
           S VY NSRML+GLA+QGNAP+AL  VD+RGVP   I +SAL T  CV++NYL P  A GL
Sbjct: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360

Query: 362 LMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIML 421
           LMALVV+ALV+NWA+ISL H+K R+A    G    F +  +P+ NWICL FMA +LVI+ 
Sbjct: 361 LMALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420

Query: 422 MTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451
           MTPG+++SV+L+P WL+V+  GY+FK + A
Sbjct: 421 MTPGLSVSVWLVPAWLVVMWAGYVFKRRRA 450


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: 749
Number of extensions: 38
Number of successful extensions: 1
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: 461
Length adjustment: 33
Effective length of query: 424
Effective length of database: 428
Effective search space:   181472
Effective search space used:   181472
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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