Align Monocarboxylic acid transporter (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__BFirm:BPHYT_RS25605 Length = 516 Score = 394 bits (1011), Expect = e-114 Identities = 214/532 (40%), Positives = 321/532 (60%), Gaps = 37/532 (6%) Query: 20 ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGI 79 +L I +F++ + VT+ + + T +++FY G + S +NG A+AGD++SAA+FLG Sbjct: 3 LLTIVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFLGF 62 Query: 80 VGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAAC 139 G +SL G DG LY++ A+LV L+L+AEP+RN GR+T DV++ R+++ R+A Sbjct: 63 SGLVSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLATIV 122 Query: 140 GTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQ 199 GT+ V L Y++ QMAGAG+L+ ++L + V V +VGI MI YVL GGM TT+VQ Sbjct: 123 GTVVVNLAYMVPQMAGAGALIKLMLGVP----YDVAVVLVGIGMIVYVLFGGMIATTWVQ 178 Query: 200 MIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQY 259 ++KA+LL+ ++ + V L +VE+ S A+ GY Sbjct: 179 IVKAMLLLVAACVLVSMLLAAVRFNPLALFA-SVERLYGSKMLASGGY------------ 225 Query: 260 GATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLV 319 LD +SL ++ G AGLPH++ RFYTVP A+ ARKSV W + L G+F+++T + Sbjct: 226 ---FHHPLDTMSLFISFIFGVAGLPHIMTRFYTVPDARTARKSVLWLMFLAGSFFMVTTL 282 Query: 320 LGYGAAALVGPDRVIAAPGAANAAAPLLAF-------ELGGSIFMALISAVAFATVLAVV 372 +G+ +A VG D + AA N A PLLA LGG IF+A I A+AFA +LAVV Sbjct: 283 IGFASAVFVGQDAIRAADKGGNLALPLLAQYLGGGAGSLGGQIFLASICAIAFAAILAVV 342 Query: 373 AGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFL 432 AGL + +S A+ HD+Y V+R G ++AEQVRV+RI V +G+ +I L +LA NV L Sbjct: 343 AGLTLASSGAIAHDLYVNVLRKGAVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVL 402 Query: 433 VALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVP 492 V LA +VAAS+N P IL S++W++FNT G + + GL S++ L F+ PA G+ Sbjct: 403 VILAISVAASSNFPIILLSIFWRRFNTAGVIGGVIGGLTSSVALAFVGPAFMGSH----- 457 Query: 493 GADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE-MEVRSLTGV 543 A+FP+ NP +VS+P+ + W+ T++ +P D E +R+ TG+ Sbjct: 458 ----ALFPIVNPAIVSLPIGLFSAWLCTMLSRPTPTQDGDFEAFYLRAQTGI 505 Lambda K H 0.324 0.138 0.393 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: 623 Number of extensions: 31 Number of successful extensions: 5 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: 551 Length of database: 516 Length adjustment: 35 Effective length of query: 516 Effective length of database: 481 Effective search space: 248196 Effective search space used: 248196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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