Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate WP_012383191.1 BIND_RS00890 MFS transporter
Query= TCDB::M1Q159 (468 letters) >NCBI__GCF_000019845.1:WP_012383191.1 Length = 467 Score = 436 bits (1121), Expect = e-127 Identities = 220/445 (49%), Positives = 302/445 (67%), Gaps = 13/445 (2%) Query: 12 GIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPF 71 G+ ++FASS GT+IEWYDF+++G+LA + FY P+ ++ + TFA GF VRP Sbjct: 15 GLKFLVFASSLGTMIEWYDFFLYGSLAVFFSELFYPKDNPVAALLISVATFATGFAVRPL 74 Query: 72 GAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLAL 131 GA++FG +GD +GRK T+LIT+ +MG T LIG+LPT +G A ++L+ +R++QGLAL Sbjct: 75 GAVLFGHLGDRIGRKTTFLITLLLMGGATALIGILPTYASVGLLAPVLLVVLRLIQGLAL 134 Query: 132 GGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWR 191 GG+YGGAAT+VAEHAP G+RG +TS IQT A+ G +SL V+L R LG+A F WGWR Sbjct: 135 GGEYGGAATYVAEHAPDGRRGGWTSAIQTMASMGFFVSLAVVLSCRFLLGDAIFASWGWR 194 Query: 192 LPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGA 251 +PF+ S +LV+LSL R L ESP+F QLK VSK+P++ESFA+P N R +L LFG Sbjct: 195 IPFLLSAVLVMLSLGARLRLAESPIFLQLKAEDRVSKSPVRESFADPRNRRLMLAVLFGV 254 Query: 252 TMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKKV 311 GQ V +YT FYAL++LQ I + SNL++ +L+ MP FV FG SD+IGRK + Sbjct: 255 ASGQAVTFYTANFYALYFLQSILKVDFLTSNLVMVLGVLIGMPLFVLFGIWSDKIGRKPL 314 Query: 312 MLSGMLLAVLTYYPIYGLM-AAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYG 370 +++GM AV+ PI+ +M +A P G N +L VF+ V VYG Sbjct: 315 IIAGMAAAVVLLVPIFMVMQSAVGPQ-----------GINIWLLAACVFVLVAIAAAVYG 363 Query: 371 PIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAG 430 P AA+LVE+FP +IRYTS+S+PYHIGNG+FGG +P+IGL L+ ATGN AGL +P+A+ Sbjct: 364 PYAAYLVEVFPPQIRYTSLSIPYHIGNGIFGGFLPLIGLSLVAATGNPLAGLIYPIAVCV 423 Query: 431 ICLVVGFLLIKETNKVDISDASTSI 455 I +++G L + ET I D TS+ Sbjct: 424 INVIIGSLYLPETLHTPI-DGRTSV 447 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: 742 Number of extensions: 50 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: 468 Length of database: 467 Length adjustment: 33 Effective length of query: 435 Effective length of database: 434 Effective search space: 188790 Effective search space used: 188790 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 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