GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Porphyrobacter dokdonensis DSW-74

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_068865628.1 I603_RS12870 cation acetate symporter

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



>NCBI__GCF_001677335.1:WP_068865628.1
          Length = 591

 Score =  776 bits (2004), Expect = 0.0
 Identities = 396/600 (66%), Positives = 468/600 (78%), Gaps = 37/600 (6%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           MD Q+L YL VG +FALYIGIAIWSRAGST EFYVAGGGV+PV+NGMATAADWMSAASFI
Sbjct: 1   MDTQSLIYLFVGASFALYIGIAIWSRAGSTSEFYVAGGGVNPVVNGMATAADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           S+AGI++F GYD SVYLMGWTGGYVLLAL +APYLRKFG+FTVPDFIG RYYS+AAR VA
Sbjct: 61  SMAGIIAFTGYDASVYLMGWTGGYVLLALLLAPYLRKFGQFTVPDFIGTRYYSKAARVVA 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V+C I + FTYIAGQMRGVG+VFSRFL+V++ TGV IGM +VF Y+VLGGMKGITYTQVA
Sbjct: 121 VICLILVSFTYIAGQMRGVGIVFSRFLDVDITTGVVIGMGIVFVYSVLGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240
           Q+CVLIFA+MVPA F+S M+TG+ +PQ G G+++ DA    +G+Y+L+KLD +   LGF+
Sbjct: 181 QFCVLIFAYMVPAFFLSFMITGNPVPQFGLGSKVGDA----SGLYVLQKLDLVLTGLGFA 236

Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300
            YT G K MIDVF IT ALM GTAGLPHVIVRFFTVPK  DAR+SAGWAL+FIA++YTT 
Sbjct: 237 AYTAGQKSMIDVFCITLALMVGTAGLPHVIVRFFTVPKASDARLSAGWALIFIALLYTTA 296

Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGE-- 358
           PA+ AF+R+N IE++N       AY  AP W  NWE   LI + DKN DG + Y KG+  
Sbjct: 297 PAVGAFARLNFIESVNEQ-----AYAQAPAWFTNWEGNDLIAFADKNGDGVMQYRKGDAF 351

Query: 359 --------------------------TNEMKIDRDIMVLATPEIANLPAWVIALVAAGGL 392
                                      NE+ +D+DIMVLA PEI  LP WVIALVAAGGL
Sbjct: 352 TGKPEFTGETGASGERLVVNPPVTDNANEVYVDQDIMVLANPEIGKLPGWVIALVAAGGL 411

Query: 393 AAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPG 452
           AAALST+AGLLLVIS +VSHDLLK+ F P IS+K ELL AR+AA   I +AGY GINPPG
Sbjct: 412 AAALSTAAGLLLVISAAVSHDLLKQTFRPAISEKGELLAARLAATAAIGVAGYLGINPPG 471

Query: 453 FVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGD 512
           +VA VVA AFGLAA+SLFPAI+MGIFS+ MN+EGAIAGMV GL F+  YI++FK V+P  
Sbjct: 472 WVAQVVAFAFGLAAASLFPAILMGIFSKRMNREGAIAGMVSGLAFTFGYIVWFKLVSPDT 531

Query: 513 NNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572
           + A+NWLFGISPEGIG++GM INFAVA  VS +TAA P  +  +V+SIR P+GAGEA  H
Sbjct: 532 STAANWLFGISPEGIGVIGMAINFAVATAVSGITAAPPSEIARLVDSIRVPRGAGEAQVH 591


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: 1208
Number of extensions: 53
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: 572
Length of database: 591
Length adjustment: 36
Effective length of query: 536
Effective length of database: 555
Effective search space:   297480
Effective search space used:   297480
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 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