Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 442 bits (1137), Expect = e-129 Identities = 232/370 (62%), Positives = 284/370 (76%), Gaps = 4/370 (1%) Query: 7 RPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLA 66 +P KT+ + LL+I ++K +D AVDDVSLTI KGEIFALLG SG GKSTLLRMLA Sbjct: 10 KPTTKTQDEV--LLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLA 67 Query: 67 GFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEI 126 GFE+P+ G+I LDG D++ +PPY RPINMMFQSYALFPHMTVEQNIAFGLKQDK+ KA+I Sbjct: 68 GFERPTEGRIYLDGQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADI 127 Query: 127 ASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRD 186 + RV EML LVHM+++AKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR Sbjct: 128 SQRVQEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRT 187 Query: 187 RMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYS 246 +MQLEVV+ILERVGVTCVMVTHDQEEAMTMAGRIAIM+ G Q+G P +IYE P +R Sbjct: 188 QMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMI 247 Query: 247 AEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLC 305 AEFIG+VN+F+ + E + D +L SP L P + + +++ V +A+RPEK ++ Sbjct: 248 AEFIGTVNLFDCEIIEDEADHAILKSPTLPQPFLIGHGVTTSLEDKHVWLAVRPEKTLIT 307 Query: 306 EEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRL 365 E P N+A G+V IAYLG LSVY+++L+ ++I + N R R PTWGD++ + Sbjct: 308 REQPEGEYNWARGKVHDIAYLGGLSVYYIKLEDDKIIQCSMTNTER-RADHPTWGDDIYI 366 Query: 366 CWEVDSCVVL 375 WE S VVL Sbjct: 367 SWEATSGVVL 376 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: 425 Number of extensions: 8 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: 378 Length adjustment: 30 Effective length of query: 347 Effective length of database: 348 Effective search space: 120756 Effective search space used: 120756 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: 50 (23.9 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