Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate RR42_RS27720 RR42_RS27720 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS27720 Length = 440 Score = 263 bits (673), Expect = 7e-75 Identities = 150/436 (34%), Positives = 246/436 (56%), Gaps = 27/436 (6%) Query: 12 GIWKVIFASSAGTVIEWYDFYIFGALATTLASK-FYNTGTPIGDIIAWLGTFAVGFLVRP 70 G+ ++ AS+ GT +EWYDF ++ +A + + F+ + P+ I T+AVG++ RP Sbjct: 21 GMGRLAAASTIGTTLEWYDFTVYNLMAALVFNAVFFPSFDPLTGTILAFSTYAVGYVSRP 80 Query: 71 FGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLA 130 G ++FG +GD +GR+F + T+ +MG T L+G+LPT G W+ I+L+ +R LQG A Sbjct: 81 LGGVLFGHLGDKLGRRFVLVATLILMGVATGLMGVLPTYMSWGIWSPILLVALRFLQGAA 140 Query: 131 LGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGW 190 +GG++ GA EH Q +RG S+ Q + G L+ G I + + L DF WGW Sbjct: 141 IGGEWAGAVLLSMEHGEQHQRGRNASFTQVGPSCGTLLGTGFIAVVSLWLSPEDFQAWGW 200 Query: 191 RLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFG 250 R+PF++S+LLV+ LW+R+ ++E+PLF++++ K+ +K P+KE F + + L+ G Sbjct: 201 RVPFLSSVLLVLFGLWLRKGVEETPLFKEMEARKSTAKTPIKEVFVDHWRR---LLVAGG 257 Query: 251 ATMGQGVVWYTGQFYALFYLQKI--FNTPLIDSNLIVGAAL-LLSMPFFVFFGSLSDRIG 307 +G V++ + L Y+ + + PL S ++GAA +++P FGSLSD++G Sbjct: 258 VRIGSDVLYALVVVFTLTYVTSVLHLSRPLALSATMIGAACNAIAVP---LFGSLSDKLG 314 Query: 308 RKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTM 367 R+ V ++G +LAV+ + + LM D Q P+ + V + +I M Sbjct: 315 RRPVYIAGAVLAVVWAFVFFRLM------DSAQ----------PLQICAAVVVGLIIHAM 358 Query: 368 VYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMA 427 +YGP AAF+ E FPT++RY SL Y + V GG P+I L + G+ A + A Sbjct: 359 MYGPQAAFVTEQFPTRVRYAGSSLAYTLAGIVGGGFAPLIIASLYKSYGSTLAISLYVSA 418 Query: 428 IAGICLVVGFLLIKET 443 + L V L+ +ET Sbjct: 419 AVALTL-VALLVARET 433 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: 598 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 468 Length of database: 440 Length adjustment: 33 Effective length of query: 435 Effective length of database: 407 Effective search space: 177045 Effective search space used: 177045 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