GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Megamonas funiformis YIT 11815

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_008539556.1 HMPREF9454_RS09855 sodium/proline symporter PutP

Query= SwissProt::P07117
         (502 letters)



>NCBI__GCF_000245775.1:WP_008539556.1
          Length = 501

 Score =  483 bits (1244), Expect = e-141
 Identities = 245/494 (49%), Positives = 330/494 (66%), Gaps = 25/494 (5%)

Query: 1   MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60
           M+ +  ++V F +Y+  M+ IG   +  T N  DYILGGR LG +VT++SA ASDMSGW+
Sbjct: 1   MSDNISIIVAFLLYLLFMMAIGVYFYYRTHNMSDYILGGRKLGAWVTSMSAEASDMSGWM 60

Query: 61  LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120
           LMGLPG  +L+G++  WIA+GL LG W NW+ +A RLR +TE  NN+LTLPD+   R+ D
Sbjct: 61  LMGLPGFAYLAGLNAGWIAVGLALGTWANWQFIARRLRKYTELANNSLTLPDFLQNRYHD 120

Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180
           KS ++R++ A+ IL+FF IY +SG VAG +LF + FG+ YE AL  GA   + YTF+GGF
Sbjct: 121 KSPLIRVVMAIFILIFFIIYTSSGFVAGGKLFNTIFGIPYEYALCLGAFVIVFYTFVGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGL------- 233
           LAV WTD +Q  +M FA+++ P+    ++GGFGD+   I   SI N +            
Sbjct: 181 LAVCWTDFIQGVMMFFAILIVPIAAAFTLGGFGDTYTAI---SITNPEFFNPFTKSDGSY 237

Query: 234 -NFVAIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFG 292
              + +ISL+ WGLGYFGQPHIL RFMA  S   +  A RI+MTW+++ L  AV VG  G
Sbjct: 238 TTVLELISLLAWGLGYFGQPHILVRFMAITSSSELKKATRIAMTWVVISLTAAVCVGMVG 297

Query: 293 IAYFNDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSA 352
             Y      L G    N+E VF+ +   LF+P+ AGI+LSA+LAA+MST S QLLV +SA
Sbjct: 298 SVYLT--TPLNGT---NSETVFLVMTDHLFSPFWAGIVLSAVLAAIMSTASAQLLVGASA 352

Query: 353 ITEDLYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAF 412
           + +DLYK F+ K  + +ELV V R+ V+ +AL+AIAL  +P N +L +V+YAWAGFGA F
Sbjct: 353 VAQDLYKQFIHKDINPRELVLVTRLSVIGIALIAIALGLDPNNSILNIVAYAWAGFGATF 412

Query: 413 GPVVLFSVMWSRMTRNGALAGMIIGALTVIVWKQ---------FGWLGLYEIIPGFIFGS 463
           GP +LFS+ W R TRNG LAGMI+G +TV+VWKQ         +  L LYEI+PGFI  S
Sbjct: 413 GPALLFSLFWRRTTRNGILAGMIVGGITVLVWKQITLLDIATVYPILQLYEIVPGFILSS 472

Query: 464 IGIVVFSLLGKAPS 477
           + I++ S L KAPS
Sbjct: 473 LAIIIGSKLDKAPS 486


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: 708
Number of extensions: 38
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: 501
Length adjustment: 34
Effective length of query: 468
Effective length of database: 467
Effective search space:   218556
Effective search space used:   218556
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.

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