Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate SMa1328 SMa1328 MtbA protein
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Smeli:SMa1328 Length = 440 Score = 419 bits (1076), Expect = e-121 Identities = 209/439 (47%), Positives = 294/439 (66%), Gaps = 12/439 (2%) Query: 10 PKGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVR 69 P +VI A+S G +IEWYDFYIFG+LA L+ KF+ P+ +++ + F GFL+R Sbjct: 6 PTDFRRVIVAASVGNIIEWYDFYIFGSLAAVLSVKFFEQSHPVAALLSTIALFTAGFLIR 65 Query: 70 PFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGL 129 P GA +FG +GD VGRK+T+LIT+T MG T IGL+PT + +G A +L ++R++QGL Sbjct: 66 PLGAFLFGWMGDRVGRKYTFLITLTGMGLGTGAIGLIPTYESIGLTAAFLLFSLRMIQGL 125 Query: 130 ALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWG 189 LGG+YGGA T+VAEH P +RG+YT W+QT+ T G+++SL VI+ R G F+ W Sbjct: 126 CLGGEYGGAITYVAEHVPDERRGYYTGWLQTSPTLGIVVSLAVIIAARTYFGSEAFDAWA 185 Query: 190 WRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALF 249 WR+PF+ S LLV ++++IR L+E+P+FQ++K +++NP +E+F + N+++V IA Sbjct: 186 WRVPFLVSFLLVGIAIYIRLQLQETPIFQEIKAKGQMTQNPWREAFLSS-NIKYVGIATI 244 Query: 250 GATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRK 309 +GQGVVWY+GQF+AL++LQ++ ++S IVGAALLL+ P + FG LSD IGRK Sbjct: 245 -VLIGQGVVWYSGQFWALYFLQQVSKVDPLNSAYIVGAALLLATPSLILFGWLSDIIGRK 303 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369 V+L GMLLA LTYYP+Y + A D N I ++FI V YV MVY Sbjct: 304 PVILGGMLLAALTYYPLYLWLGAVTQPD----------NINYPIAIFIIFILVCYVGMVY 353 Query: 370 GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIA 429 GP+ AFL E FP +IRYTS+S+PYHIGNG GGLVP I ATG+ L +P+A+ Sbjct: 354 GPVGAFLAEYFPGRIRYTSVSVPYHIGNGWGGGLVPFITSAAFAATGSIGYALIYPIAVP 413 Query: 430 GICLVVGFLLIKETNKVDI 448 +C V+ L+ ET ++ I Sbjct: 414 AVCFVLAIFLMPETRRISI 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: 735 Number of extensions: 38 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: 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