Align ABC transporter permease (characterized, see rationale)
to candidate PP_5195 PP_5195 putative Iron ABC transporter, permease protein
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__Putida:PP_5195 Length = 540 Score = 73.9 bits (180), Expect = 8e-18 Identities = 69/228 (30%), Positives = 107/228 (46%), Gaps = 17/228 (7%) Query: 83 WSGILVDPQWWNAVRNTLYFTVVSVGLEV-VLGLLVALLLNI-KFTGRALVRALILIPWA 140 WS +L D Q + NTL VV VG+ V VLG+ +A L ++ F GR + +++P+A Sbjct: 39 WSHLL-DTQMGRLLGNTLTL-VVGVGIGVTVLGVSLAWLTSLCDFPGRRWLDWALMLPFA 96 Query: 141 IPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFV 200 IP V A ++ +L+ + + L G + P S VI V V P+V Sbjct: 97 IPAYVLAFVFVGLLDFAGPVQSALREVFGPMRLPRV------RSTGGVITVLVLVFYPYV 150 Query: 201 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 260 LL A EAARV G+ PL+ FWRV LP+ PA+ ++++L F + Sbjct: 151 YLLARTAFLAQGKGLMEAARVLGLSPLQAFWRVALPMARPAIGAGIALALMETLADFGAV 210 Query: 261 YVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLY 308 V ++ +T + + SAA L++AV+ +LY Sbjct: 211 AVFNFDTFTTAIYKTW-------YGFFSLSSAAQLASLLLLAVMLVLY 251 Lambda K H 0.329 0.140 0.443 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: 403 Number of extensions: 23 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: 320 Length of database: 540 Length adjustment: 31 Effective length of query: 289 Effective length of database: 509 Effective search space: 147101 Effective search space used: 147101 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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