Aligments for a candidate for Shew_2731 in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for Shew_2731 in Shewanella oneidensis MR-1

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate 201983 SO2857 sodium/solute symporter family protein (NCBI ptt file)

Query= reanno::PV4:5209923
         (572 letters)



>lcl|FitnessBrowser__MR1:201983 SO2857 sodium/solute symporter
           family protein (NCBI ptt file)
          Length = 578

 Score = 1001 bits (2589), Expect = 0.0
 Identities = 496/578 (85%), Positives = 539/578 (93%), Gaps = 6/578 (1%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           M VQ LTYLIVG +FALYIGIA+W+RAGSTKEFYVAGGGVHPV+NGMATAADWMSAASFI
Sbjct: 1   MGVQGLTYLIVGLSFALYIGIALWTRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDF+G+RYYSQAARTVA
Sbjct: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFLGERYYSQAARTVA 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V+CAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFY+VLGGMKGITYTQVA
Sbjct: 121 VICAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYSVLGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240
           QYCVLIFAFMVPAIF+SVMMTGHI+PQ+GFGA+L+DAAGNN+GVYLL+KL+ LS  LGF+
Sbjct: 181 QYCVLIFAFMVPAIFLSVMMTGHIIPQIGFGAQLLDAAGNNSGVYLLDKLNNLSVDLGFA 240

Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300
            YT+GSK MIDV  ITGALM GTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT+
Sbjct: 241 PYTDGSKSMIDVLCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTV 300

Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGE-- 358
           PALAAFSRVNMIETINGP+  GVAYETAP+WIKNWEKTGLIKWDDKN DGKIYYA G+  
Sbjct: 301 PALAAFSRVNMIETINGPDQKGVAYETAPNWIKNWEKTGLIKWDDKNGDGKIYYATGKIE 360

Query: 359 ----TNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL 414
               TNEMKID DI+VLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL
Sbjct: 361 DAASTNEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL 420

Query: 415 LKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAII 474
           LKKN MP+ISDK+EL+YAR+AA +GIV+AGYFG+NPPGFVAAVVA AFGLAASSLFPAII
Sbjct: 421 LKKNLMPNISDKKELMYARLAAGIGIVIAGYFGVNPPGFVAAVVAFAFGLAASSLFPAII 480

Query: 475 MGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWLFGISPEGIGMLGMII 534
           MGIFS+TMNKEGAIAGM++GL F++ YI+YFKF++P  N  +NW  GISPEGIGM+GM+I
Sbjct: 481 MGIFSKTMNKEGAIAGMILGLFFTSGYIVYFKFIDPTANVPANWFLGISPEGIGMVGMVI 540

Query: 535 NFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572
           NF VA IVSKVTAA P +V +MVESIRFPKGAGEA DH
Sbjct: 541 NFVVAAIVSKVTAATPVHVQEMVESIRFPKGAGEASDH 578


Lambda     K      H
   0.326    0.140    0.423 

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: 1311
Number of extensions: 43
Number of successful extensions: 2
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: 572
Length of database: 578
Length adjustment: 36
Effective length of query: 536
Effective length of database: 542
Effective search space:   290512
Effective search space used:   290512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources