Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 191 bits (486), Expect = 2e-53 Identities = 114/331 (34%), Positives = 180/331 (54%), Gaps = 22/331 (6%) Query: 19 LLEIRNLTKSYDG--QHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQI 76 LL++ ++K + Q AV D+ + I +G + A++G +G GK+TLL+++AG E P G+I Sbjct: 3 LLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEI 62 Query: 77 MLDGVDL----SQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNE 132 + G + S +P R + ++FQ YALFP MT+ +N+ L Q+ +IA + Sbjct: 63 VFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAM---D 119 Query: 133 MLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEV 192 L L +++ PHQLS GQRQR ALAR+LA RPKLLLLD+P +LD + ++ + ++ Sbjct: 120 SLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDI 179 Query: 193 VDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS 252 DI++ G+T ++ +H ++A+++A IAI+++G Q+G P EIY+ P Y A F G Sbjct: 180 RDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGK 239 Query: 253 VNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANG 312 N +L EDG + HP AS D V + KI E P +G Sbjct: 240 RN---ELLATPTEDGFYAGFGFIPHP----DSASYTDKVKILFRSEDAKIKKSTEQPLSG 292 Query: 313 CNFAVGEVIHIAYLGDLSVYHVRLKSGQMIS 343 V + + GD + + G+ IS Sbjct: 293 I------VTRVLFYGDHQIVKLEDDEGKQIS 317 Lambda K H 0.321 0.137 0.400 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: 270 Number of extensions: 13 Number of successful extensions: 3 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: 377 Length of database: 345 Length adjustment: 29 Effective length of query: 348 Effective length of database: 316 Effective search space: 109968 Effective search space used: 109968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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