Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 288 bits (736), Expect = 2e-82 Identities = 153/323 (47%), Positives = 212/323 (65%), Gaps = 9/323 (2%) Query: 20 LEIRNLTKSYDGQH----AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQ 75 +E+RN++K Y A+D+VS+ I E F LLG SGCGK+TLLR +AGFE S G+ Sbjct: 7 IEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDGE 66 Query: 76 IMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLG 135 I L G ++ +PP+ R +N +FQSYALFPHM+V QNIAFGL+ L + I RV+EML Sbjct: 67 IRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEMLA 126 Query: 136 LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDI 195 LV MQ AKRKP +LSGGQ+QRVALAR+LA +PK+LLLDEP+ ALD KLR MQ+E+ + Sbjct: 127 LVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKRV 186 Query: 196 LERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNV 255 + G+T + VTHDQEEA+T++ RIA+M+ GK +QIG P EIYE P ++ A+FIG +N Sbjct: 187 QKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGDINF 246 Query: 256 FEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNF 315 G +K Q++ + G+ P+++ A D V +A RPE+ L E + Sbjct: 247 LPGHIKRGQQNEKLFVPNGM--PVEIPCPAQGFDGSKVQLAFRPERSQLVEPTQPHHLR- 303 Query: 316 AVGEVIHIAYLGDLSVYHVRLKS 338 G + + Y+G ++Y RL + Sbjct: 304 --GVIEAVLYVGTATLYQCRLNN 324 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: 393 Number of extensions: 15 Number of successful extensions: 1 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: 361 Length adjustment: 30 Effective length of query: 347 Effective length of database: 331 Effective search space: 114857 Effective search space used: 114857 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