GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctP in Burkholderia phytofirmans PsJN

Align Na+/solute symporter (characterized, see rationale)
to candidate BPHYT_RS06030 BPHYT_RS06030 sodium:solute symporter

Query= uniprot:B2T7V3
         (493 letters)



>FitnessBrowser__BFirm:BPHYT_RS06030
          Length = 516

 Score =  533 bits (1374), Expect = e-156
 Identities = 277/497 (55%), Positives = 352/497 (70%), Gaps = 24/497 (4%)

Query: 7   VNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVGGDFYTA 66
           +N +A  VF+ FF+ VT++GF AA W+RGDL  L EWGLGGR+FGT+++WFL+GGD YTA
Sbjct: 1   MNAIATFVFVLFFIGVTILGFIAAHWRRGDLAHLEEWGLGGRRFGTIVTWFLLGGDLYTA 60

Query: 67  YTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKIAHAKNHITAADYVQGEYGG 126
           YT IAVPALV+  GA GFFALPYTI++YPF F V PKLW IA  + ++T+AD+V   YG 
Sbjct: 61  YTFIAVPALVFGAGATGFFALPYTILIYPFAFVVFPKLWSIAKRQGYVTSADFVSARYGS 120

Query: 127 KWFPAAVAITGIVATMPYIALQLVGMQVVIKGL-----GVTGEMPLIVAFVILALYTYAS 181
           +    A+A+TGIVATMPYIALQLVG++VVI  L     G  G++PLI+AF ILA YTY S
Sbjct: 121 RMLALAIAVTGIVATMPYIALQLVGIEVVIGALGFDTKGFVGDLPLIIAFAILAAYTYTS 180

Query: 182 GLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDA---ADTYFKAKGGATGIILK 238
           GLRAPAMIA VKD++IYI + AA+ +IP +LGG+ H+F     A    KA       +  
Sbjct: 181 GLRAPAMIAVVKDVLIYITIFAAIIVIPPQLGGFGHIFSVVPPAKLLLKAPD-----VSS 235

Query: 239 PTQFTAYASLALGSALAAFMYPHTMTAVLSSSSANTVRKNAIFLPAYTLLLGLIALLGYM 298
              ++AYA+LA+GSALA F+YPH++TAVLSS S NT+R+N   LPAY+L+LGL+ALLG+M
Sbjct: 236 LNGYSAYATLAVGSALALFLYPHSITAVLSSKSGNTIRRNMAMLPAYSLVLGLLALLGFM 295

Query: 299 AIAAGV----------HVKSASDMVPALFNTLFPSWFVGFAAAAIAISALVPAAIMSIGA 348
           A+A+GV               +  VPALF   FPSWFVG A AAI I ALVPAAIMSI A
Sbjct: 296 ALASGVKDMPEFAPYFKAFGPNFAVPALFLHYFPSWFVGVAFAAIGIGALVPAAIMSIAA 355

Query: 349 ANLFTRNLWRPLVSPNISPEGEASTAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWI 408
           ANL+TRN+ +  V+ N++ E E + AK+VSL+VK GA+ FI+ LP  YAI LQLLGG+WI
Sbjct: 356 ANLYTRNIHKEFVNRNMTHEQETNVAKLVSLIVKVGAVAFILGLPLTYAIQLQLLGGIWI 415

Query: 409 LQIFPAIVFSLYTRRLNTPGLFLGWLAGIVLGTGLAISQGLK-PVFALHLGDAVYPVYIG 467
           +Q  PAIV  LYTR L+  GL  GW  GI  GT +AIS  L   +F +HL     P Y  
Sbjct: 416 IQTLPAIVLGLYTRVLDYRGLLAGWAVGIATGTWMAISLKLAGSIFTIHLFGMAIPGYAA 475

Query: 468 LIALTVNIVVSFVVSVL 484
           + +L VN+VV+ VVS+L
Sbjct: 476 VWSLIVNLVVAVVVSLL 492


Lambda     K      H
   0.328    0.141    0.431 

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: 868
Number of extensions: 46
Number of successful extensions: 5
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: 493
Length of database: 516
Length adjustment: 34
Effective length of query: 459
Effective length of database: 482
Effective search space:   221238
Effective search space used:   221238
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 (21.8 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 (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