Align ABC transporter permease (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 165 bits (418), Expect = 1e-45 Identities = 103/294 (35%), Positives = 156/294 (53%), Gaps = 16/294 (5%) Query: 27 RAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANL---ADTGGGTFIGFGNYLFHNGSSW 83 RAAWLFL P LL L L P++ SLTD +L AD F+ GNY W Sbjct: 5 RAAWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNY-------W 57 Query: 84 SGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTG-RALVRALILIPWAIP 142 +L P +W+A+ +TLYF +V V L +V L ALLLN + L R + P Sbjct: 58 E-LLHRPLFWSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTT 116 Query: 143 TIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTL 202 + A IW ++ N ++G+ N+ + LG+ P+ W D +M +I+ VWK + + Sbjct: 117 VVAVAVIWRYLFNTKYGLANYALGGLGI--HPVDWLGDPRWAMPTIILFAVWKNFGYNMI 174 Query: 203 LMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYV 262 + LAALQ +P+D YEAAR+DG PL+ F +TLP+L P LL+ I + ++F +V Sbjct: 175 IFLAALQAIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFV 234 Query: 263 LTSNS--SSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRR 314 +T ST S+ + ++ ++G SA + LLFL++ + + L + RR Sbjct: 235 MTEGGPLQSTTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLRVARR 288 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: 246 Number of extensions: 14 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: 320 Length of database: 292 Length adjustment: 27 Effective length of query: 293 Effective length of database: 265 Effective search space: 77645 Effective search space used: 77645 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