GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Methanospirillum lacunae Ki8-1

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_109968238.1 DK846_RS07180 sodium/proline symporter PutP

Query= SwissProt::P07117
         (502 letters)



>NCBI__GCF_003173355.1:WP_109968238.1
          Length = 496

 Score =  471 bits (1211), Expect = e-137
 Identities = 237/487 (48%), Positives = 328/487 (67%), Gaps = 10/487 (2%)

Query: 7   MLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPG 66
           ++  F VY+  M+ IG + +R T N  DYILG R L  +V +LSA ASDMSGWLL+GLPG
Sbjct: 8   IITAFVVYLAVMLSIGALYYRKTHNVSDYILGSRGLNKYVASLSAEASDMSGWLLIGLPG 67

Query: 67  AVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILR 126
             ++SG+   W+A+GL LG ++NWKLVA RLR++T+   ++LTLP++F  RFEDKS I+ 
Sbjct: 68  LAYVSGMQAGWVALGLILGTFLNWKLVAKRLRIYTQSAGDSLTLPEFFKNRFEDKSDIIG 127

Query: 127 IISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWT 186
            I A+ IL+FF +Y ++  V+  +LF + FG+ Y TAL  G+   ++YTFIGGF+AV WT
Sbjct: 128 GICAIFILIFFLLYTSAQFVSTGKLFNTVFGIDYTTALLIGSLIVVVYTFIGGFMAVCWT 187

Query: 187 DTVQASLMIFALILTPVIVIISVGG---FGDSLEVIKQKSIENVDMLKG--LNFVAIISL 241
           D  Q  LM+FA+++ P+  +  +GG     DS+  +    +     + G  L  +AIISL
Sbjct: 188 DFFQGLLMLFAILVVPIAAVGLLGGPVATIDSINAVNPNLLNPFTGVDGTPLTAIAIISL 247

Query: 242 MGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPA 301
           M WGLGYFGQPHIL RFMA      I HAR ++M W+IL L  AVA+G  G   F   P 
Sbjct: 248 MAWGLGYFGQPHILVRFMAIRDPKEIAHARTVAMIWVILSLTAAVAIGLVG-KVFLSQPL 306

Query: 302 LAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAF 361
           +  A    +E VF+ +   +F  ++AGI+L  ILAA+MST S QLLV SSA++EDLY+ +
Sbjct: 307 VGSA----SETVFMVMTDQIFFSFLAGIILCGILAAIMSTASSQLLVTSSAVSEDLYRTY 362

Query: 362 LRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVM 421
           LR HAS+KE +WV R+ VLV A++AI L  NP++ V G+VSYAWAGFGAAFGP +L ++ 
Sbjct: 363 LRPHASEKEGIWVSRISVLVAAIIAIILGLNPDSLVYGIVSYAWAGFGAAFGPALLMALF 422

Query: 422 WSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAMQ 481
           W RMT+ GALAG+I G +TV++WKQ    GLYEI+PGFI   + I V S++  AP +++ 
Sbjct: 423 WRRMTKAGALAGIISGGVTVLIWKQLNLFGLYEIVPGFIIALVAIYVVSIITPAPDSSIV 482

Query: 482 KRFAEAD 488
             F + +
Sbjct: 483 TVFDDVE 489


Lambda     K      H
   0.328    0.140    0.436 

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: 724
Number of extensions: 43
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: 502
Length of database: 496
Length adjustment: 34
Effective length of query: 468
Effective length of database: 462
Effective search space:   216216
Effective search space used:   216216
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 (21.8 bits)
S2: 52 (24.6 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