GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctP in Paraburkholderia bryophila 376MFSha3.1

Align Monocarboxylate transport permease protein (characterized)
to candidate H281DRAFT_03156 H281DRAFT_03156 solute:Na+ symporter, SSS family

Query= SwissProt::Q1M7A2
         (491 letters)



>FitnessBrowser__Burk376:H281DRAFT_03156
          Length = 493

 Score =  629 bits (1623), Expect = 0.0
 Identities = 318/488 (65%), Positives = 379/488 (77%), Gaps = 2/488 (0%)

Query: 5   INGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGGDFYT 64
           +N  A+ VFI FFVLVTV+GF A+RW++ + L  + EWGLGGR FGT I+WFLVGGDFYT
Sbjct: 7   VNPVAMTVFIAFFVLVTVIGFFAARWKRGD-LTQLHEWGLGGRQFGTVISWFLVGGDFYT 65

Query: 65  AYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVHGQYG 124
           AYTVIAVPALVY+VGAYGFFALPYTI+VYPFVF VMP LWK A    ++TA D VHG+YG
Sbjct: 66  AYTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKVAHAKNHITAADYVHGEYG 125

Query: 125 SRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLHGELPLAIAFIVLALYTYSAGLRA 184
            +    AVA TG++ATMPYIALQLVGM  V+K LG+ GELPL +AF++LALYTY++GLRA
Sbjct: 126 GKWFPAAVALTGIVATMPYIALQLVGMQVVIKGLGVTGELPLIVAFVILALYTYASGLRA 185

Query: 185 PALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQAKGSGN-LLLGGNQYVAY 243
           PA+IAFVKDIMIYIVVIAAV LIP+KLGGYA+VF +AD  F+AKG    ++L   Q+ AY
Sbjct: 186 PAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDAADTYFKAKGGATGIILKPTQFTAY 245

Query: 244 ATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYMGHAANLK 303
           A+LALGSALAAFMYPHT+T + +S+S  T+RKNAI LPAYTLLLGL+ALLGYM  AA + 
Sbjct: 246 ASLALGSALAAFMYPHTMTAVLSSSSATTVRKNAIFLPAYTLLLGLIALLGYMAIAAGVH 305

Query: 304 LDSANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVDPDV 363
           + SA+D+VPTLF TLF  WF GFA AAIAI ALVPAA+MSIGAANLFTRN W+  V P++
Sbjct: 306 VKSASDIVPTLFGTLFPSWFVGFAAAAIAISALVPAAIMSIGAANLFTRNLWRPLVSPNI 365

Query: 364 SDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWILQTLPALVFGLYTNWFR 423
           +   EA  AKI SLVVK GALL I+FLPTQ+A+DLQLLGG+WILQ  PA+VF LYT    
Sbjct: 366 TPEAEASNAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWILQIFPAIVFSLYTRRLN 425

Query: 424 APGLLAGWFVGFGGGTFLVWDAGWKPLHLISLGGEPFTVYTGLLALAANIAVAVVVNALL 483
            PGL AGW VG   GT L    G KP+  + LG   + +Y GL+AL  NI V  VV+A+ 
Sbjct: 426 TPGLFAGWLVGIVLGTALAISQGLKPVFALHLGDAVYPIYIGLIALVVNIVVTFVVSAVS 485

Query: 484 PAKAPVRA 491
           P +  V A
Sbjct: 486 PRRVAVSA 493


Lambda     K      H
   0.327    0.142    0.439 

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: 841
Number of extensions: 52
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: 491
Length of database: 493
Length adjustment: 34
Effective length of query: 457
Effective length of database: 459
Effective search space:   209763
Effective search space used:   209763
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 (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