Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate PP_1458 PP_1458 putative inner membrane metabolite transport protein YhjE
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Putida:PP_1458 Length = 432 Score = 230 bits (586), Expect = 8e-65 Identities = 146/445 (32%), Positives = 232/445 (52%), Gaps = 42/445 (9%) Query: 15 KVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 +V AS GT IE+YDFY++ A A + F+ +G+ ++A TF + FL RP G+ Sbjct: 19 RVATASFIGTAIEFYDFYVYATAAALVIGPVFFPSGSGTAQMLAAFLTFGIAFLARPLGS 78 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 +FG GD +GRK T + ++ +MG T IG+LP D +G WA IIL +R QGL LGG Sbjct: 79 ALFGHFGDRIGRKSTLVASLLLMGVSTTAIGVLPGYDSIGVWAPIILCLLRFGQGLGLGG 138 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGAA E+AP+GKR ++ + Q + G L + G+ L + L + F EWGWR+P Sbjct: 139 EWGGAALLATENAPEGKRAWFGMFPQLGPSIGFLAANGLFLTLALVLSDEQFREWGWRIP 198 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNP-LKESFANPYNLRWVLIALFGAT 252 F+ S LV++ L++R L+ESP+F KAV+++ +K + ++ W+ L A Sbjct: 199 FLLSAALVLVGLYVRLKLEESPVF-----AKAVARHERVKMPVVDLFSKYWLPTLLGAAA 253 Query: 253 MGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFF--VFFGS-------LS 303 M VV YALFY+ +F+ + L L + F VF LS Sbjct: 254 M---VV-----CYALFYISTVFSLSYGVTTLGYSRETFLGLLCFAVVFMALATPLSAWLS 305 Query: 304 DRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVI 363 DR GRK V++ G LLA+ + + + L+ + + + L + I++ Sbjct: 306 DRYGRKPVLIVGGLLAIASGFTMEPLLTSGSTAG----------------VALFLAIELF 349 Query: 364 YVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLW 423 + + + P+ A L ELFPT +RYT S Y++G V P L++ G + G + Sbjct: 350 LMGVTFAPMGALLPELFPTHVRYTGASAAYNLGGIVGASAAPFFAQKLVSMGGLSWVGGY 409 Query: 424 WPMAIAGICLVVGFLLIKETNKVDI 448 +++A + ++ L +KET + Sbjct: 410 --VSVAAVISLIAVLCLKETRNTTL 432 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: 633 Number of extensions: 36 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: 432 Length adjustment: 33 Effective length of query: 435 Effective length of database: 399 Effective search space: 173565 Effective search space used: 173565 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