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_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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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