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.
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:
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