GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pantoea rwandensis LMG 26275

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_084935516.1 HA51_RS15470 sodium/proline symporter PutP

Query= SwissProt::P07117
         (502 letters)



>NCBI__GCF_002095475.1:WP_084935516.1
          Length = 494

 Score =  831 bits (2146), Expect = 0.0
 Identities = 407/493 (82%), Positives = 456/493 (92%)

Query: 1   MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60
           M++STPMLVTF +YI GM+LIGF+A+RSTK+FDDYILGGRSLG  VTALSAGASDMSGWL
Sbjct: 1   MSVSTPMLVTFVIYILGMVLIGFVAYRSTKSFDDYILGGRSLGSVVTALSAGASDMSGWL 60

Query: 61  LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120
           LMGLPGA+FLSGISESWIAIGLT+GAW+NWK+VAGRLRV TE+++NALTLPD+F+ RFED
Sbjct: 61  LMGLPGAIFLSGISESWIAIGLTIGAWLNWKIVAGRLRVQTEHHDNALTLPDFFSSRFED 120

Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180
           KS++LR+ISA+VIL+FFTIYCASG+VAGARLFESTFGM Y+TALWAGAAATILYT +GGF
Sbjct: 121 KSKLLRVISAVVILIFFTIYCASGVVAGARLFESTFGMDYQTALWAGAAATILYTLVGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS 240
           LAVSWTDTVQASLMIFALILTPV VII+VGG  DSL VI+ KS+EN+DMLKGLNFVA+IS
Sbjct: 181 LAVSWTDTVQASLMIFALILTPVFVIIAVGGLDDSLAVIEAKSLENLDMLKGLNFVAVIS 240

Query: 241 LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP 300
           L+GWGLGYFGQPHILARFMAADSH SI  ARRI MTWMILCLAGAVAVGFFGIA+F +HP
Sbjct: 241 LLGWGLGYFGQPHILARFMAADSHRSIRAARRIGMTWMILCLAGAVAVGFFGIAFFQNHP 300

Query: 301 ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA 360
            LA  V+QN ERVFIELA+ILFNPWIAGILLSAILAAVMSTLSCQLLVCSSA+TEDLYK 
Sbjct: 301 ELAAGVSQNGERVFIELARILFNPWIAGILLSAILAAVMSTLSCQLLVCSSALTEDLYKG 360

Query: 361 FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV 420
           FLRK+ASQKELVWVGR+MVLV+AL+AIALAANPENRVLGLVSYAWAGFGAAFGPVVLF V
Sbjct: 361 FLRKNASQKELVWVGRLMVLVIALIAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFGV 420

Query: 421 MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM 480
            W RMTRNGALAGM+IGA+TV++WKQ+G++ LYEIIPGFIF SI IVVFSL+G  PS A 
Sbjct: 421 CWKRMTRNGALAGMVIGAMTVLLWKQYGYVELYEIIPGFIFASIAIVVFSLIGNGPSEAA 480

Query: 481 QKRFAEADAHYHS 493
           Q RFA A+A Y +
Sbjct: 481 QARFAAAEAEYQT 493


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: 934
Number of extensions: 42
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: 494
Length adjustment: 34
Effective length of query: 468
Effective length of database: 460
Effective search space:   215280
Effective search space used:   215280
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