Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_043828657.1 RSPH17029_RS19050 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000015985.1:WP_043828657.1 Length = 360 Score = 289 bits (740), Expect = 7e-83 Identities = 157/360 (43%), Positives = 221/360 (61%), Gaps = 9/360 (2%) Query: 18 PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 P+ E+RN+TK Y A +++L I GE + LG SGCGK+T LRMLAGFEQ S GQ++ Sbjct: 5 PIAELRNVTKRYGLVTAATNLTLAIEPGEFLSFLGPSGCGKTTALRMLAGFEQASEGQVL 64 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQ--DKLPKAEIASRVNEMLG 135 +DG D + +P + RP+NM+FQ YALFPH+TV QN+ +GL Q K P+AE+A+ V E L Sbjct: 65 IDGRDATALPAWQRPVNMVFQQYALFPHLTVAQNVGYGLNQRRPKPPRAEVAAAVEEALA 124 Query: 136 LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDI 195 LV + F R+ +LSGGQ+QRVALAR++ +PK+LLLDEPM ALDKKLR MQ+E+ + Sbjct: 125 LVQLSGFGARRTWELSGGQQQRVALARAIVNKPKILLLDEPMAALDKKLRHDMQIELKSL 184 Query: 196 LERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNV 255 +G+T V+VTHDQEEA++M+ RI IM+ G QIG PEE+Y+ P +RY A+F+G N Sbjct: 185 QRELGITFVLVTHDQEEALSMSDRIVIMDHGCIAQIGGPEELYDRPQSRYVADFVGRSNF 244 Query: 256 FEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNF 315 + R+ + LV ++ GL+ + PV ++LRPE+I L P G Sbjct: 245 IGATGRGREAEILVAEAGGLI--FNARGGEKIAPGSPVTLSLRPEEIRLA--PSGEGHRM 300 Query: 316 AVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVL 375 V H +LG+ + YH+ + + A + L G EV W + + L Sbjct: 301 V---VTHRIFLGEHTEYHLTSGALPHLVAVVPRTAEAGSALLAPGSEVMASWRDGAALAL 357 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: 339 Number of extensions: 14 Number of successful extensions: 2 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: 360 Length adjustment: 30 Effective length of query: 347 Effective length of database: 330 Effective search space: 114510 Effective search space used: 114510 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 Apr 10 2024. 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