Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 158 bits (399), Expect = 4e-43 Identities = 90/217 (41%), Positives = 135/217 (62%), Gaps = 5/217 (2%) Query: 18 PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 P+LE++ + KSY + D+ L I GE A+LG SG GK+TL+ ++AG +P AG+++ Sbjct: 2 PILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVL 61 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLK--QDKLPKAEIASRVNEMLG 135 L G + P R + +FQSY+L P +TVE NIA + KAE +RV + +G Sbjct: 62 LRGKPVDG-PGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIG 118 Query: 136 LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDI 195 +V + A+R+P +LSGG RQRVA+AR+LA P +LLLDEP+ ALD R ++Q E+ I Sbjct: 119 MVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAI 178 Query: 196 LERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIG 232 E+ T +++T+D +EA+ +A RI +N G G Sbjct: 179 WEQEKKTVILITNDVDEALLLADRIIPLNPGPGATFG 215 Score = 138 bits (347), Expect = 4e-37 Identities = 87/238 (36%), Positives = 132/238 (55%), Gaps = 19/238 (7%) Query: 35 VDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPIN 94 VD L +++GE +L+G SGCGKST+L M AG S G ++LDG ++S+ P Sbjct: 312 VDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREVSEAGPDRA--- 368 Query: 95 MMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASR---VNEMLGLVHMQEFAKRKPHQLS 151 ++FQ+ +LFP +T QN+A G+ + P A A R V+ L V + + +K +S Sbjct: 369 VVFQAPSLFPWLTALQNVALGVDR-VYPHASPAERLDIVSYYLERVGLGDSMDKKASDMS 427 Query: 152 GGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQE 211 G RQRV +AR+ A PKLLLLDEP G LD R +Q ++++ R VT + VTHD + Sbjct: 428 NGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAICVTHDVD 487 Query: 212 EAMTMAGRIAIMNRGKFVQIGE-----------PEEIYEHPT-TRYSAEFIGSVNVFE 257 EA+ +A ++ +M G +IG+ + EHP Y AE + ++ +E Sbjct: 488 EAILLADKVVMMTNGPNARIGKVLNVDIPRPRTRRALLEHPRYYEYRAEVLNFLDEYE 545 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: 522 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 553 Length adjustment: 33 Effective length of query: 344 Effective length of database: 520 Effective search space: 178880 Effective search space used: 178880 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: 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