GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Oscillibacter ruminantium GH1

Align L-proline uptake porter, PutP (characterized)
to candidate WP_040664283.1 ON16_RS13915 sodium/proline symporter

Query= TCDB::Q9I5F5
         (506 letters)



>NCBI__GCF_000307265.1:WP_040664283.1
          Length = 509

 Score =  372 bits (956), Expect = e-107
 Identities = 207/511 (40%), Positives = 301/511 (58%), Gaps = 29/511 (5%)

Query: 2   SVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWLL 61
           S N   +IT ++Y+  +V IG+A  R      D+ LGGR LG  VTA+SA ASDMS WLL
Sbjct: 3   SANICIVITILVYLIVVVGIGVACSRRNRTTDDFYLGGRKLGPLVTAMSAEASDMSSWLL 62

Query: 62  MGLPGAVYLSGLSES-WIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120
           MGLPG  YLSG++++ W AIGL  G YLNWL VA R+R+ T H   A+T+P++F+ RF D
Sbjct: 63  MGLPGVAYLSGVADAGWTAIGLAAGTYLNWLIVARRIRLYT-HRVGAITIPEFFSKRFGD 121

Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180
             R+L   +A+VIL+FF  Y ASG  A  +LF S FG+ Y  A+       +AYT +GGF
Sbjct: 122 ERRILTGIAAVVILIFFIPYTASGFAACGKLFNSLFGIDYVGAMVVSGIIIVAYTTLGGF 181

Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVE---------PTFTAIELKDATSFDMLK 231
           LA S TD +Q+ +M  AL +  +  + A GG++         P + ++ L    + +   
Sbjct: 182 LAASTTDFIQSIVMTIALFVMVLFGIRAAGGLDVVMDNARALPGYLSMTLSHDMAANAAN 241

Query: 232 GASFIGVISLMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFF 291
              FI ++S +AWGLGYFG PHIL RFMA +  + +  +RR++  W+++ +  A+ +G  
Sbjct: 242 PYGFITIVSTLAWGLGYFGMPHILLRFMAIEDERKLKLSRRVASIWVVISMAVAIFIGIV 301

Query: 292 GIAYFQAHPEQAGAVS----ENPERVFIELAKILFNPWI-----AGVLLSAILAAVMSTL 342
           G         +AG +        E V + LA +L    I     AGV+L+ ILA+ MST 
Sbjct: 302 GYGV-----TKAGGIGFLEGSASETVIVRLAGLLSTYGIPAALLAGVVLAGILASTMSTS 356

Query: 343 SCQLLVCSSALTEDFYKAFLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVS 402
             QLL  +S+++++      +   ++ + V   R  V+ +A+IA+++A NP + V G+VS
Sbjct: 357 DSQLLAAASSVSQNLMSECFQVKMNEKKKVTAARLTVVGIALIAMFMARNPNSSVFGIVS 416

Query: 403 YAWAGFGAAFGPLVLFSLLWKRMTRNGALAGMIVGAATVILWKNLL----GWTGLYEIIP 458
           +AWAGFGAAFGP+VLF L WKR    GALAGM+ G   + +WK L+    G   +YE++P
Sbjct: 417 FAWAGFGAAFGPVVLFGLFWKRTNWQGALAGMVSGGVMIFVWKYLVRPLGGVWNIYELLP 476

Query: 459 GFLFASVAIVVFSLLGKAPSTSMLKRFDDAE 489
            FL A V IV  SL   AP   ++  F+D +
Sbjct: 477 AFLVACVFIVAVSLATTAPKQEIVDTFNDVK 507


Lambda     K      H
   0.326    0.138    0.421 

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: 765
Number of extensions: 43
Number of successful extensions: 7
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: 506
Length of database: 509
Length adjustment: 34
Effective length of query: 472
Effective length of database: 475
Effective search space:   224200
Effective search space used:   224200
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 (21.7 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