Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AZOBR_RS19470 AZOBR_RS19470 DL-methionine transporter permease subunit
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__azobra:AZOBR_RS19470 Length = 221 Score = 207 bits (526), Expect = 2e-58 Identities = 105/200 (52%), Positives = 143/200 (71%) Query: 17 IWLASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSLVVNILRSLPF 76 ++ A +DT +M+ S L LGLPLGVLL +TG ++ + A + ++VN+ RS PF Sbjct: 9 LFKALLDTLYMVAVSGLLGTALGLPLGVLLAVTGRGELLQNLAFNRVAGVLVNMTRSTPF 68 Query: 77 IILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEATQAMGA 136 IIL++ +IP T LI GTS+G A AI PL V A PF AR+VE A+REVD+G+IEA Q+MGA Sbjct: 69 IILVVAIIPFTRLIAGTSIGTAAAIVPLTVAAVPFIARIVEGAVREVDRGLIEAAQSMGA 128 Query: 137 STRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIRFGYQRFQTDV 196 + QII LLPEA P I +T++ ++L+ Y+AM G VG GGLGDL IR+GYQRF +V Sbjct: 129 TPFQIIRKVLLPEAMPAIALGLTLSVVSLIGYSAMVGAVGGGGLGDLGIRYGYQRFLPEV 188 Query: 197 MVVTVVMLLILVQILQTVGD 216 M+ VV+L++LVQI+Q+ GD Sbjct: 189 MLAVVVVLIVLVQIVQSTGD 208 Lambda K H 0.329 0.143 0.419 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: 139 Number of extensions: 7 Number of successful extensions: 1 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: 225 Length of database: 221 Length adjustment: 22 Effective length of query: 203 Effective length of database: 199 Effective search space: 40397 Effective search space used: 40397 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: 46 (22.3 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