GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Escherichia coli BW25113

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 15139 b1015 proline:sodium symporter (NCBI)

Query= SwissProt::P07117
         (502 letters)



>FitnessBrowser__Keio:15139
          Length = 502

 Score =  991 bits (2562), Expect = 0.0
 Identities = 502/502 (100%), Positives = 502/502 (100%)

Query: 1   MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60
           MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL
Sbjct: 1   MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60

Query: 61  LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120
           LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED
Sbjct: 61  LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120

Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180
           KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF
Sbjct: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS 240
           LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS
Sbjct: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS 240

Query: 241 LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP 300
           LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP
Sbjct: 241 LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP 300

Query: 301 ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA 360
           ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA
Sbjct: 301 ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA 360

Query: 361 FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV 420
           FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV
Sbjct: 361 FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV 420

Query: 421 MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM 480
           MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM
Sbjct: 421 MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM 480

Query: 481 QKRFAEADAHYHSAPPSRLQES 502
           QKRFAEADAHYHSAPPSRLQES
Sbjct: 481 QKRFAEADAHYHSAPPSRLQES 502


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: 1097
Number of extensions: 46
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: 502
Length of database: 502
Length adjustment: 34
Effective length of query: 468
Effective length of database: 468
Effective search space:   219024
Effective search space used:   219024
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 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