GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03156 H281DRAFT_03156
           solute:Na+ symporter, SSS family
          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 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