Align Monocarboxylic acid transporter (characterized)
to candidate WP_109969114.1 DK846_RS11580 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_003173355.1:WP_109969114.1 Length = 502 Score = 400 bits (1028), Expect = e-116 Identities = 218/504 (43%), Positives = 315/504 (62%), Gaps = 23/504 (4%) Query: 21 LNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIV 80 L ++FV+ + T+ + + ++ FYT G NG+A AGDYLSAASFLGI Sbjct: 8 LAFTIFVLITLSTLALSFYAARRVRTASHFYTAGGGVKWFVNGIAFAGDYLSAASFLGIA 67 Query: 81 GAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACG 140 G I+ +G+DGF+YSIGF W+VALL++AEPLR +G+FT D L++R K +R+ AA Sbjct: 68 GMIAFSGFDGFMYSIGFLAGWIVALLIIAEPLRKIGKFTFGDALAWRFASKKIRLCAALS 127 Query: 141 TLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQM 200 L V++FYLI QM GAGS++ L+ + ++A V+ IVG V+I V GM TTYVQ Sbjct: 128 ALVVSIFYLIPQMVGAGSIIQPLIGL---PYEAGVI-IVGAVVILIVATAGMVSTTYVQF 183 Query: 201 IKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYG 260 IK LL+ +TV G ++ + A + A+ + PG+++ Sbjct: 184 IKGFLLLIAAGALTVGVLAVAGMGPLEFISTVLNSPAITVPASNGTVTGDVFMTPGMKF- 242 Query: 261 ATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVL 320 LDF SLAL L LGTA LPH+L+R++TVPT +ARKS AI+ IG FY++TL L Sbjct: 243 ---KNPLDFASLALGLILGTAALPHILIRYFTVPTPADARKSTVVAIIAIGVFYVLTLFL 299 Query: 321 GYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAITAS 380 G GA + D P +N +APLLA +GG F A+I+++AFAT+L V+GL I A+ Sbjct: 300 GLGANYFMTVD-----PKNSNLSAPLLAEFIGGEWFFAIIASIAFATILGTVSGLIIAAA 354 Query: 381 AAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVA 440 A+ HDIY V+ +S + + +R+S++T V +G+I+I+LGI++ QNVAFLV LAFA+A Sbjct: 355 GAIAHDIYTEVM-GRRSDDKKALRISKLTAVTVGVIAIILGIISKGQNVAFLVGLAFAIA 413 Query: 441 ASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWAIFP 500 ASAN+P ++ +L+WK+ G +A I TGL+ ++ LI +SP V G A+FP Sbjct: 414 ASANIPALICTLFWKRSTERGIIAGILTGLLLSVSLILISPTVMGKA---------ALFP 464 Query: 501 LKNPGLVSIPLAFIAGWIGTLVGK 524 L+NPG++SIPL F+ + +L GK Sbjct: 465 LENPGIISIPLGFLVTILVSLTGK 488 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: 626 Number of extensions: 25 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: 551 Length of database: 502 Length adjustment: 35 Effective length of query: 516 Effective length of database: 467 Effective search space: 240972 Effective search space used: 240972 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 24 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