Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PfGW456L13_929 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
Query= SwissProt::Q02UB7 (367 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_929 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2) Length = 360 Score = 429 bits (1104), Expect = e-125 Identities = 205/351 (58%), Positives = 268/351 (76%), Gaps = 3/351 (0%) Query: 17 SVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSG 76 +VA QAA +H+YNWSDYI TL F KETGIK VYDV+DSNE LE KLLAG++G Sbjct: 13 TVAVSVQAAGT--VHIYNWSDYIGETTLADFQKETGIKPVYDVFDSNETLEGKLLAGRTG 70 Query: 77 YDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTI 136 YDVVVPSN FL KQIKAG +QKLDKS+LPN+ NL+ L+ LE +DPGN +A+PY+WGT Sbjct: 71 YDVVVPSNHFLGKQIKAGAFQKLDKSQLPNYSNLDPVLLKRLEQNDPGNLYAVPYLWGTN 130 Query: 137 GIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKP 196 GIGYN DKVKA G + +DSW ++F+P+NI+KL+ CGV+FLDS E++P L+Y+G Sbjct: 131 GIGYNVDKVKAVLGVDT-IDSWGVLFEPQNIKKLQSCGVAFLDSADEMMPTVLNYMGLNA 189 Query: 197 DTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAK 256 ++ +PK+ + A L +RPYVTYFHSSKYI+DLANG+ICVAIG+SGDI+QAK+RAEEAK Sbjct: 190 NSTDPKDYEKATAKLLAVRPYVTYFHSSKYIADLANGDICVAIGFSGDIFQAKNRAEEAK 249 Query: 257 NKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNA 316 V + Y+IPKEG +FDM+AIPKD+ N + A AF+N+L+KPE++A+++D V + N N Sbjct: 250 KGVNIAYSIPKEGGALWFDMLAIPKDSANVKQAHAFINYLLKPEVIAQVSDYVGYANPNP 309 Query: 317 AATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 + L+ ++IR D +YP +EV+ K Y +LP QR MTRSWTK+KSGK Sbjct: 310 GSDKLMEQSIRTDEAVYPPQEVLDKTYVSVELPPNIQRLMTRSWTKVKSGK 360 Lambda K H 0.315 0.133 0.390 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: 476 Number of extensions: 13 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: 367 Length of database: 360 Length adjustment: 29 Effective length of query: 338 Effective length of database: 331 Effective search space: 111878 Effective search space used: 111878 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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