Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate PP_1016 PP_1016 mannose/glucose ABC transporter, permease protein
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Putida:PP_1016 Length = 302 Score = 147 bits (370), Expect = 4e-40 Identities = 88/271 (32%), Positives = 144/271 (53%), Gaps = 6/271 (2%) Query: 45 LMSIAVYGGTGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLVGF 104 ++ + YG + F +SFT L P Y L YA+ +D + A++N L+ F Sbjct: 31 IVLVGFYGYILWTFVLSFTTSTFL--PTYKWAGLAQYARLFDNDRWWVASKNLLLFGGLF 88 Query: 105 TTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLVVT 164 I L +G+ LA+LLD IR +T+YL PM+LS +VT W W+ N G+ L+ Sbjct: 89 IAISLAIGVLLAVLLDQRIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDKLLRD 148 Query: 165 T--LGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGASI 222 GF +DWL +P + +++A +WQ SG+ M ++LAGL+ + AA++DGAS+ Sbjct: 149 WGWEGFR-LDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDPSIIRAAQMDGASL 207 Query: 223 TRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAFK 282 R Y +++P L+ SA ++L A+K+F + A+ P +D+ A M F Sbjct: 208 PRIYWTVVLPSLRPVFFSALMILSHIAIKSFDLVAAMTAG-GPGYSSDLPAMFMYSFTFS 266 Query: 283 FGEWAYSAAIATMLLIMALGVIGPYLYYQYK 313 G+ +A A ++L L ++ PYLY + + Sbjct: 267 RGQMGMGSASAILMLGAILAILVPYLYSELR 297 Lambda K H 0.326 0.140 0.424 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: 278 Number of extensions: 17 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: 317 Length of database: 302 Length adjustment: 27 Effective length of query: 290 Effective length of database: 275 Effective search space: 79750 Effective search space used: 79750 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 (21.6 bits) S2: 48 (23.1 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