Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 129 bits (324), Expect = 9e-35 Identities = 93/285 (32%), Positives = 150/285 (52%), Gaps = 24/285 (8%) Query: 54 WIFLFPALFVLLLYLGYPVVETLRLSLLER-----VPGGGYQWVGLDNYAQMASEPKFWE 108 W+FL PAL VL L+ PV+ L LSL + ++V L NY ++ P FW Sbjct: 8 WLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLFWS 67 Query: 109 AMRNNMFWLIVVPALSTAFGLLAAQLTDR--IKWGNVAKSIIFMPMAISFVGASVIWKLV 166 A+ + +++++V LS L AA L + + + ++ +F P+ + V +VIW+ + Sbjct: 68 ALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWRYL 127 Query: 167 YDGRPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALR 226 ++ + G+ N + GLG PV +L P W +++ VW G+ M+I AAL+ Sbjct: 128 FNTK------YGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQ 181 Query: 227 GIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNG--- 283 IP + EAA IDGASPL+ F I +P + PT+++V ++F F MT G Sbjct: 182 AIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPL 241 Query: 284 QWETQVLANYMFDKLFRANDWGVGSASAM-----VIMLLVTPILI 323 Q T VL M+++ F+ W +GSASA+ +IM VT +++ Sbjct: 242 QSTTSVL-YLMYEEGFKW--WNLGSASAVAFLLFLIMFAVTAVML 283 Lambda K H 0.329 0.143 0.455 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: 262 Number of extensions: 15 Number of successful extensions: 5 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: 334 Length of database: 292 Length adjustment: 27 Effective length of query: 307 Effective length of database: 265 Effective search space: 81355 Effective search space used: 81355 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: 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