Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate WP_083763475.1 AMB_RS08370 MFS transporter
Query= TCDB::M1Q159 (468 letters) >NCBI__GCF_000009985.1:WP_083763475.1 Length = 445 Score = 211 bits (537), Expect = 4e-59 Identities = 133/444 (29%), Positives = 232/444 (52%), Gaps = 29/444 (6%) Query: 11 KGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRP 70 KG ++F S G ++E+YD+Y++ A + + F+ P ++ FA+GF +RP Sbjct: 25 KGKILMVFKGSVGNLVEYYDWYVYSAFSLYFSKYFFPGDDPTVQLLNTSAIFALGFFMRP 84 Query: 71 FGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLA 130 G + G D GRK L+++++M + + +I ++P + +G A I LI R+LQGL+ Sbjct: 85 LGGWLLGTHADRKGRKAALLVSVSMMCAGSLIIAVMPGYNSIGVAAPIALILARLLQGLS 144 Query: 131 LGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVIL-ITRISLGEADFNEWG 189 LGG+YG AAT+++E A + +RGFY+S+ T G L++LGV++ + R+ L A+ WG Sbjct: 145 LGGEYGSAATYLSEIATKDRRGFYSSFQYVTLIMGQLLALGVLMALQRVFLTTAELEAWG 204 Query: 190 WRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALF 249 WR+PF+ L I+++++R +++E+ F+ K + V ++ ++ +P ++ + Sbjct: 205 WRIPFVIGGLCAIVAIYLRSSMEETESFEHHKGDR-VGESRIRALMRHPRE----VLTVI 259 Query: 250 GATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRK 309 G TMG V +YT Y YL D+ +I AA + M G +SD++GR+ Sbjct: 260 GLTMGGTVAFYTFTTYMQKYLVNTAGFSKSDATMISAAATFVYMLMHPLVGHISDKVGRR 319 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369 V+++ +++ L PI + A T F + ++ G Y Sbjct: 320 AVLIAFGVMSTLCTVPI---LTALGQTHDSVTAFFLVLSGLTIVSG-------------Y 363 Query: 370 GPIAAFL-VELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAI 428 I A + ELFP +IR + LP+ IG +FGG I L + GN+ W+ + Sbjct: 364 SAINAVVKAELFPVQIRALGVGLPFAIGVSLFGGTAEYIAL-WFKSMGNE---TWFYWYV 419 Query: 429 AGICL--VVGFLLIKETNKVDISD 450 G CL ++ F+ +K+T K + D Sbjct: 420 TGCCLCGLLLFVGMKDTKKTSLID 443 Lambda K H 0.328 0.144 0.450 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: 566 Number of extensions: 32 Number of successful extensions: 4 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: 468 Length of database: 445 Length adjustment: 33 Effective length of query: 435 Effective length of database: 412 Effective search space: 179220 Effective search space used: 179220 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: 51 (24.3 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