GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putP in Shewanella sp. ANA-3

Align L-proline uptake porter, PutP (characterized)
to candidate 7024259 Shewana3_1451 sodium/proline symporter (RefSeq)

Query= TCDB::Q9I5F5
         (506 letters)



>lcl|FitnessBrowser__ANA3:7024259 Shewana3_1451 sodium/proline
           symporter (RefSeq)
          Length = 483

 Score =  515 bits (1326), Expect = e-150
 Identities = 270/481 (56%), Positives = 336/481 (69%), Gaps = 12/481 (2%)

Query: 1   MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60
           M++ TP LITFV Y+  M+ IG  AYR+T+   DYILGGR +G  VTALS GASDMSGWL
Sbjct: 1   MTIETPILITFVGYLVLMMGIGFWAYRATDTVDDYILGGRKMGPAVTALSVGASDMSGWL 60

Query: 61  LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120
           L+GLPGAVYL GL E+WI IGL+VGA+LNWLFVA RLR+ T+   NALTLPD+F  RF D
Sbjct: 61  LLGLPGAVYLGGLGEAWIGIGLVVGAWLNWLFVAKRLRIYTQLADNALTLPDFFEKRFHD 120

Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180
               L++ SA+ ILVFFT Y +SG+V GA LFE  FGL Y  AL  G+A  + YTFIGGF
Sbjct: 121 KQGYLKLVSAVTILVFFTFYASSGMVGGAILFEKVFGLDYTVALVIGSAIIVGYTFIGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKG-ASFIGVI 239
            AVSWTD  Q  LM+ AL++ P  V         +   IE  D     ++    + IG++
Sbjct: 181 FAVSWTDFFQGCLMLIALLIIPFAVF----SHPESHAGIESIDPAMLALISDKTTVIGLL 236

Query: 240 SLMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAH 299
           SL+AWGLGYFGQPHIL+RFMA  +  ++P +RRI+M+WM+L L GA+A G  G  YF   
Sbjct: 237 SLLAWGLGYFGQPHILSRFMAIGTADALPLSRRIAMSWMMLSLIGALATGLAGSLYFANQ 296

Query: 300 PEQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYK 359
           P        N E VFI LA+  FNPWI G+L++AIL+A+MST+  QLLVCSS +TEDFY+
Sbjct: 297 P------LANAETVFIHLAQAAFNPWIGGLLIAAILSAIMSTIDSQLLVCSSVITEDFYR 350

Query: 360 AFLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFS 419
            +LR  A   EL+ VGR  VL +AVIA  +A NPE+ VL LVSYAWAGFGAAFGP+VL S
Sbjct: 351 KWLRPQADDRELMMVGRMGVLAIAVIAGIIALNPESSVLSLVSYAWAGFGAAFGPVVLLS 410

Query: 420 LLWKRMTRNGALAGMIVGAATVILWKNLLGWT-GLYEIIPGFLFASVAIVVFSLLGKAPS 478
           L WK+ +RNGA+A +IVGA TV++WK L G    LYEI+PGF+FA +A VV S + +   
Sbjct: 411 LFWKQYSRNGAIATIIVGALTVVIWKQLTGGIFDLYEILPGFVFAIIAGVVVSKMSRPAE 470

Query: 479 T 479
           T
Sbjct: 471 T 471


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: 845
Number of extensions: 40
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: 506
Length of database: 483
Length adjustment: 34
Effective length of query: 472
Effective length of database: 449
Effective search space:   211928
Effective search space used:   211928
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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