GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Echinicola vietnamensis KMM 6221, DSM 17526

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily

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



>FitnessBrowser__Cola:Echvi_1267
          Length = 567

 Score =  786 bits (2031), Expect = 0.0
 Identities = 398/579 (68%), Positives = 471/579 (81%), Gaps = 19/579 (3%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           MD+ T TY++VG +FALYIGIAIWSRAGSTKEFYVAGGGV P+ NGMAT ADWMSAASFI
Sbjct: 1   MDILTWTYILVGLSFALYIGIAIWSRAGSTKEFYVAGGGVSPLANGMATGADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           S+AG++SF+GYDGSVYLMGWTGGYVLLAL +APYLRKFGKFTVPDF+GDRYYS  AR VA
Sbjct: 61  SMAGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVA 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V CAIFI FTY+AGQMRGVG+VFSR+LEV+++TGV IGM +VFFYAVLGGMKGITYTQVA
Sbjct: 121 VFCAIFISFTYVAGQMRGVGIVFSRYLEVDINTGVIIGMCIVFFYAVLGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240
           QYCVLIFAFMVPAIFIS+ +T + +PQLG G  + D      G YLL+KLDG+   LGF 
Sbjct: 181 QYCVLIFAFMVPAIFISMQLTSNPIPQLGLGGTVAD------GTYLLDKLDGVLTDLGFH 234

Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300
            YT G K M D+F IT ALM GTAGLPHVIVRFFTVP+VKDAR+SAG+ALVFIAI+YTT 
Sbjct: 235 AYTSGKKSMGDMFAITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYTTA 294

Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKI-YYAKGET 359
           PA++AF   N I++++         +  P+W+ NW++T LIK +DKN DG + Y A  E 
Sbjct: 295 PAVSAFGIYNAIDSVSEK-----PIDDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPER 349

Query: 360 NEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNF 419
           NE  ID+DIMVLA PEIA LP WV+ LVAAGG+AAALST+AGLLLVISTSVS D L KNF
Sbjct: 350 NEFTIDKDIMVLANPEIAQLPNWVVGLVAAGGMAAALSTAAGLLLVISTSVSRD-LAKNF 408

Query: 420 MPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFS 479
            P ISDK+ELL AR+AAA+ +++AGYFG+NPPGFVA VVA AFGLAA+S FP IIMGIFS
Sbjct: 409 NPGISDKKELLIARVAAAVAVIVAGYFGVNPPGFVAEVVAFAFGLAAASFFPVIIMGIFS 468

Query: 480 RTMNKEGAIAGMVIGLLFSASYIIYFKFVN-----PGDN-NASNWLFGISPEGIGMLGMI 533
           + MNKEGAI GM++GL+F+ SYIIYFKF       P ++  A +W FGISPEGIG +GM+
Sbjct: 469 KRMNKEGAIWGMLVGLVFTLSYIIYFKFGTDLFGIPAESLTAEHWWFGISPEGIGSIGMV 528

Query: 534 INFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572
           +NF V+F+VS+VT A P+ V +MVE IR P+GAG+A  H
Sbjct: 529 LNFLVSFVVSRVTPAPPEAVQEMVEDIRIPRGAGQAQGH 567


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: 1170
Number of extensions: 52
Number of successful extensions: 6
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: 567
Length adjustment: 36
Effective length of query: 536
Effective length of database: 531
Effective search space:   284616
Effective search space used:   284616
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.

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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