Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate N515DRAFT_2307 N515DRAFT_2307 molybdate/tungstate transport system ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Dyella79:N515DRAFT_2307 Length = 331 Score = 135 bits (341), Expect = 1e-36 Identities = 89/238 (37%), Positives = 128/238 (53%), Gaps = 22/238 (9%) Query: 50 LLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVE 109 LLGASG GK+ LL +AG I G +PP R + + Q +ALFPH+ Sbjct: 25 LLGASGEGKTLLLSAIAGL-------IAARGEPFDGLPPQQRAVGYLPQGHALFPHLRAW 77 Query: 110 QNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPK 169 +N+AF L+ A + + L V M A+R P LSGGQ+QRVALAR+LA+RP Sbjct: 78 ENVAFSLRG-----ARRREQAMQWLERVGMAGLAERWPASLSGGQQQRVALARALARRPS 132 Query: 170 LLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFV 229 LLLLDEP ALD RD + E++ + + G+ + V+HD A +A R+ +M+ + V Sbjct: 133 LLLLDEPTSALDPVTRDEVLAELIAEVHQAGIPALAVSHDPALA-AVADRLVLMHGRRIV 191 Query: 230 QIGEPEEIYEHPTTRYSAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASV 287 QIG PE ++ P + A +G NV + G ++ +PG +ADAS+ Sbjct: 192 QIGTPEAVHAQPASGAVARLLGLRNV---------QRGRIVGAPGAQRLSWPEADASL 240 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: 320 Number of extensions: 16 Number of successful extensions: 4 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: 331 Length adjustment: 29 Effective length of query: 348 Effective length of database: 302 Effective search space: 105096 Effective search space used: 105096 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