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

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_00283 H281DRAFT_00283 solute:Na+ symporter, SSS family

Query= SwissProt::Q1M7A2
         (491 letters)



>FitnessBrowser__Burk376:H281DRAFT_00283
          Length = 516

 Score =  504 bits (1297), Expect = e-147
 Identities = 272/508 (53%), Positives = 348/508 (68%), Gaps = 28/508 (5%)

Query: 5   INGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGGDFYT 64
           +N  A  VF+ FF+ VT++GF+A+ WR+ + LAH++EWGLGGR FGT +TWFL+GGD YT
Sbjct: 1   MNAIATFVFVLFFIGVTILGFIAAHWRRGD-LAHLEEWGLGGRRFGTIVTWFLLGGDLYT 59

Query: 65  AYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVHGQYG 124
           AYT IAVPALV+  GA GFFALPYTI++YPF F+V P LW  AK  GYVT+ D V  +YG
Sbjct: 60  AYTFIAVPALVFGAGATGFFALPYTILIYPFAFVVFPKLWSIAKRQGYVTSADFVSARYG 119

Query: 125 SRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLH-----GELPLAIAFIVLALYTYS 179
           SR L LA+A TG++ATMPYIALQLVG+  V+ ALG       G+LPL IAF +LA YTY+
Sbjct: 120 SRMLALAIAVTGIVATMPYIALQLVGIEVVIGALGFDTKGFVGDLPLIIAFAILAAYTYT 179

Query: 180 AGLRAPALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAA---FQAKGSGNLLLG 236
           +GLRAPA+IA VKD++IYI + AA+ +IP +LGG+ ++FA+   A    +A    +L   
Sbjct: 180 SGLRAPAMIAVVKDVLIYITIFAAIIVIPPQLGGFGHIFATVPPAKLLLKAPDVSSL--- 236

Query: 237 GNQYVAYATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYM 296
            N Y AYATLA+GSALA F+YPH++T + +S SG TIR+N  MLPAY+L+LGLLALLG+M
Sbjct: 237 -NGYSAYATLAVGSALALFLYPHSITAVLSSKSGNTIRRNMAMLPAYSLVLGLLALLGFM 295

Query: 297 GHAANL----------KLDSANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGA 346
             A+ +          K    N  VP LF   F  WF G AFAAI IGALVPAA+MSI A
Sbjct: 296 ALASGVKDMPEFAPYFKAFGPNFAVPALFLHFFPSWFVGVAFAAIGIGALVPAAIMSIAA 355

Query: 347 ANLFTRNFWKAYVDPDVSDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWI 406
           ANL+TRN  K +V+ +++   E  VAK+ SL+VKVGA+  I+ LP  +A+ LQLLGGIWI
Sbjct: 356 ANLYTRNIHKEFVNRNMTHEQETNVAKLVSLIVKVGAVAFILGLPLTYAIQLQLLGGIWI 415

Query: 407 LQTLPALVFGLYTNWFRAPGLLAGWFVGFGGGTFLVWD---AGWKPLHLISLGGEPFTVY 463
           +QTLPA+V GLYT      GLL GW VG   GT++      AG   +  I L G     Y
Sbjct: 416 IQTLPAIVLGLYTRVLDYRGLLLGWAVGIATGTWMAVSLKLAG--SIFTIHLFGMAIPGY 473

Query: 464 TGLLALAANIAVAVVVNALLPAKAPVRA 491
             + +L  N+ VAVVV+ L+ A    RA
Sbjct: 474 AAVWSLIVNLVVAVVVSLLVRAFGMQRA 501


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: 824
Number of extensions: 50
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: 491
Length of database: 516
Length adjustment: 34
Effective length of query: 457
Effective length of database: 482
Effective search space:   220274
Effective search space used:   220274
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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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources