Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS15605 BPHYT_RS15605 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS15605 Length = 316 Score = 259 bits (661), Expect = 7e-74 Identities = 141/309 (45%), Positives = 200/309 (64%), Gaps = 16/309 (5%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M+ F+QQ+LNGL LGS+Y ++A+GYTMVYGI+G+INFAHGD+ M+G AL VL + Sbjct: 1 MDIFIQQVLNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNH 60 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 F GL L++ L++A ++ + +TIERVAYRPLR + RLAPLITAIG+SI L Sbjct: 61 FPGLGNVPTLIIALIIAAIVCAAVGYTIERVAYRPLRKAPRLAPLITAIGVSILLQTLAM 120 Query: 121 VTQGPRNKPIPPM--------VSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTAL 172 + P P + + + +S+ +I+IIV+ +++ +V++T L Sbjct: 121 MIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMGGLLLLVHKTKL 180 Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGV 232 GRA RA ++ A+L+GVN + IS TF++G+ALAA+AG M YG A F GF PG+ Sbjct: 181 GRAMRAIAENPGNASLMGVNPNFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGL 240 Query: 233 KAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAY--------FTIAYKDVATFAILAFVL 284 KAFTAAVLGGIG+L GA+ GG+++GLIE L + Y F Y+DV F +L VL Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300 Query: 285 IFKPTGILG 293 +F+P+G+LG Sbjct: 301 VFRPSGLLG 309 Lambda K H 0.329 0.143 0.421 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: 366 Number of extensions: 18 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: 300 Length of database: 316 Length adjustment: 27 Effective length of query: 273 Effective length of database: 289 Effective search space: 78897 Effective search space used: 78897 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