GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TAT in Burkholderia phytofirmans PsJN

Align tryptophan permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= CharProtDB::CH_091156
         (592 letters)



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

 Score =  216 bits (551), Expect = 1e-60
 Identities = 141/435 (32%), Positives = 225/435 (51%), Gaps = 15/435 (3%)

Query: 78  LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137
           LKR LK RH+ +IA+GG+IGTGLF+GS   +   GP  +++G+AI G      +  LGE+
Sbjct: 10  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGIIAFMIMRQLGEM 68

Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197
             + PV G+F+++  ++      F+    Y + +  V   E+ A    + YW   +   +
Sbjct: 69  VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTWV 128

Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFIGAKY 257
              + +A+I +INL  V+ +GE EF F+ IK + V G I+    L+  G    +      
Sbjct: 129 SALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGGPQASITNL 188

Query: 258 WHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQVFWRILFFF 315
           W   G   +GF G+  +L V  +S GG+E+  + + E D   K +P A+ QV +RIL F+
Sbjct: 189 WSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIFY 248

Query: 316 LISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSVGNSC 375
           + SLT++  L P+ N+   GG     SPFV+           +++N V+L + LSV NS 
Sbjct: 249 ICSLTVLLSLYPW-NEVAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302

Query: 376 IFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVFNWLM 435
           ++A+SR L  +A QG  P     +DR G P + I  ++L      +V     +E    LM
Sbjct: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362

Query: 436 AIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIW-GSAYSALINCLILIA 494
           A+   A  + W  I+L+H++ R AM A G++L    F   V  W   A+ ALI  L+++A
Sbjct: 363 ALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALI--LVILA 420

Query: 495 Q---FYCSLWPIGGW 506
                  S+W +  W
Sbjct: 421 MTPGLSVSVWLVPAW 435


Lambda     K      H
   0.326    0.141    0.447 

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: 756
Number of extensions: 43
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: 592
Length of database: 461
Length adjustment: 35
Effective length of query: 557
Effective length of database: 426
Effective search space:   237282
Effective search space used:   237282
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 (21.6 bits)
S2: 52 (24.6 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