GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1894 in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894
         (432 letters)



>FitnessBrowser__BFirm:BPHYT_RS04180
          Length = 415

 Score =  374 bits (959), Expect = e-108
 Identities = 204/423 (48%), Positives = 263/423 (62%), Gaps = 15/423 (3%)

Query: 9   TVISLASL-SALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVA 67
           T++S A + S L  S   A +  S+ V+HWWTSGGE  A+ VLK  ++K G+ WKD AVA
Sbjct: 4   TLMSAAIVASTLATSAQVASAAESLSVLHWWTSGGESKAIRVLKDDMDKQGYEWKDFAVA 63

Query: 68  GGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSK-AENWDGLLS 126
           GG G+ AMT LK++ ++GN P  AQIKGP IQ+W   G+L      D+ K A +W   L 
Sbjct: 64  GGAGAAAMTALKTQVMSGNAPSAAQIKGPLIQDWADQGVLV-----DIDKSATDWKAQLP 118

Query: 127 KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGF 186
            +++ T+  +G YVA P ++HR+NWLWIN     K G  K PTT  EF+A  DK +AAG 
Sbjct: 119 AQINKTMMSKGHYVAAPFSVHRINWLWINKAALDKVG-GKPPTTWPEFFALADKFRAAGI 177

Query: 187 IALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYM 246
             +A GGQPWQD T++E VVLS  GAD Y+KA++DLDQKTL+ P+M + F   +KI GY 
Sbjct: 178 TPVARGGQPWQDMTIWETVVLS-QGADFYRKAMIDLDQKTLTSPQMLQVFQTARKIQGYF 236

Query: 247 DPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYN 306
           D    GRDWN+A A VI+G  GMQ MGDWAK E+  A K A  DY C A PGT  AFTY 
Sbjct: 237 DKGSTGRDWNLATAMVINGSGGMQFMGDWAKGEFANANKKADVDYICAAAPGTSNAFTYT 296

Query: 307 IDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDE 366
           +DS   F+    ++  +  Q  LAK  +   FQ+ FS+ KGSIPVR D+   MDK  FD 
Sbjct: 297 VDSFVFFQQNGKKEATL-GQLALAKTIMSPAFQEQFSLYKGSIPVRQDV--SMDK--FDA 351

Query: 367 CAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLAS 426
           CA+KS  D     K+    PS A     S A +GAI DVVT FMN  + DP +A  ++A+
Sbjct: 352 CAKKSYADEQTTIKSNTFFPSFAFGDVQSSATEGAITDVVTGFMNSNE-DPQEAMRKVAA 410

Query: 427 AVK 429
           A K
Sbjct: 411 AAK 413


Lambda     K      H
   0.314    0.129    0.377 

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: 527
Number of extensions: 25
Number of successful extensions: 6
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: 432
Length of database: 415
Length adjustment: 32
Effective length of query: 400
Effective length of database: 383
Effective search space:   153200
Effective search space used:   153200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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