GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pontibacillus litoralis JSM 072002

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_036832656.1 N784_RS04180 sodium/proline symporter PutP

Query= SwissProt::P07117
         (502 letters)



>NCBI__GCF_000775615.1:WP_036832656.1
          Length = 505

 Score =  554 bits (1427), Expect = e-162
 Identities = 271/504 (53%), Positives = 368/504 (73%), Gaps = 17/504 (3%)

Query: 3   ISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLM 62
           + T  +VTF VY+ GM+ IG  ++R T N  DY+LGGR LGP V ALSAGASDMSGWLL+
Sbjct: 1   MGTATVVTFVVYLLGMLGIGIASYRLTSNLSDYVLGGRRLGPGVAALSAGASDMSGWLLL 60

Query: 63  GLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKS 122
           GLPGA++ SG+SE+WI IGL +GA++NW+ VA RLR +TE  N+++T+PD+   RF D S
Sbjct: 61  GLPGAIYASGLSEAWIGIGLAIGAYLNWQFVARRLRSYTEVANDSITVPDFLENRFRDNS 120

Query: 123 RILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLA 182
            +LR++SALVIL+FFT Y +SG+VAGA+LFE++FG++YET+LW GA   I YTF+GGFLA
Sbjct: 121 HMLRVVSALVILIFFTFYTSSGMVAGAKLFEASFGLNYETSLWVGAIVIISYTFLGGFLA 180

Query: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLM 242
           VSWTD +Q  LM  ALI+ P++ I+ +GG+ + +  + + + ++++M++G+  VAIIS +
Sbjct: 181 VSWTDFIQGILMFLALIIVPIVAIMELGGWNEVVNTVGEINADHLNMVQGVGAVAIISSL 240

Query: 243 GWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPAL 302
            WGLGYFGQPHIL RFMA  S   +  AR I +TWM+L L GA+  GF G+AY  D    
Sbjct: 241 AWGLGYFGQPHILTRFMALRSAKDVPKARFIGITWMVLGLYGAIFTGFVGLAYVADEGNT 300

Query: 303 A-------GAVNQNA--------ERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLL 347
           A         V  +A        E++FI  +Q+LFNP +AGILL+AIL+A+MST+  QLL
Sbjct: 301 AKLSEFGVQLVTSDAGIQMLGDPEKIFIAFSQVLFNPIVAGILLAAILSAIMSTIDSQLL 360

Query: 348 VCSSAITEDLYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAG 407
           V SSA+ ED YKA LRK+A+ +ELVWVGR+ V V+AL+AI LA NPE+ VL LVSYAWAG
Sbjct: 361 VSSSAVAEDFYKAILRKNATDRELVWVGRLSVAVIALIAIILAYNPESSVLNLVSYAWAG 420

Query: 408 FGAAFGPVVLFSVMWSRMTRNGALAGMIIGALTVIVWKQF--GWLGLYEIIPGFIFGSIG 465
           FGAAFGP+++ S+ W  +TRNGA+AGM++GA+TVI W Q    +  LYEI+PGF+   + 
Sbjct: 421 FGAAFGPIIILSLFWKSLTRNGAMAGMVVGAITVIAWDQLVKPFFPLYEIVPGFLLCGLV 480

Query: 466 IVVFSLLGKAPSAAMQKRFAEADA 489
            +V SLL K P+  +++ F +A A
Sbjct: 481 AIVVSLLDKEPTDEIKQEFEQAKA 504


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: 777
Number of extensions: 50
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: 502
Length of database: 505
Length adjustment: 34
Effective length of query: 468
Effective length of database: 471
Effective search space:   220428
Effective search space used:   220428
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