Align ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_2943 Various polyols ABC transporter, permease component 1
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2943 Length = 316 Score = 124 bits (312), Expect = 2e-33 Identities = 90/283 (31%), Positives = 148/283 (52%), Gaps = 18/283 (6%) Query: 31 LFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGSSWSGILVDP 90 L LTP + L L PL+ T +FSL NL F G N+ F + DP Sbjct: 38 LLLTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEF--------FVTDP 89 Query: 91 QWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAIPTIVSAKIW 150 + AV NT+ + + VVLG+ +ALL+N F GR +VR L++ P+ + V+A +W Sbjct: 90 SFGTAVVNTILLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFFVMPTVNALMW 149 Query: 151 -SWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLAALQ 209 + M+N +G++ + + G AP+ W D L ++VI++ W+ +PF TL+ + ALQ Sbjct: 150 KNMMMNPIYGVLAQVWIFFGA--APVDWLTDHPL--FSVIVMVSWQWLPFATLIFMTALQ 205 Query: 210 MLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSNSSS 269 + + EA+R+DG + L+ + +P L ++ V + ++ L +F IY T+ Sbjct: 206 SMNHEQLEASRMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPG 265 Query: 270 TMSMSV---YARQHLVEFQDVGYGSAASTLLFLVVAVIALLYL 309 S +V +Q L+ F D G SA + L +V+A IA ++L Sbjct: 266 DASTNVTFLIFKQALLNF-DAGVASAGA-LFAVVLANIAAVFL 306 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: 211 Number of extensions: 15 Number of successful extensions: 3 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: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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