Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__azobra:AZOBR_RS32415 Length = 305 Score = 185 bits (469), Expect = 1e-51 Identities = 105/303 (34%), Positives = 179/303 (59%), Gaps = 21/303 (6%) Query: 3 YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFA 62 +F+QQ++NGL++G +Y L+AIG+T+++G++ ++NFAHG+++ +G F L +V+T++ Sbjct: 6 FFLQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGL---MVITAMAP 62 Query: 63 GLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRG----------SFRLAPLITAIGMS 112 L +AV+ LV+ V A+ L ER+A+RP R + R A L++++ +S Sbjct: 63 PL-LAVVPLVLAVGAVSGVGL-----ERIAFRPFRRFTDEASQKSRAMREATLLSSLAVS 116 Query: 113 ITLSNFIQVTQGPRNKPIPP--MVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRT 170 I + G + IP ++ G I V+ ++I +AV+L +++ RT Sbjct: 117 IMTREIMMHIFGGDMQGIPSGYLLQQPVAIGPIMVASGSLVIFATSAVMLGALQFLLYRT 176 Query: 171 ALGRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTP 230 G RA ++ A +G+N D+TI TF +G+ L A AG + +Y G S + GF P Sbjct: 177 QTGLGIRAVSNNQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMGFAP 236 Query: 231 GVKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTG 290 GVKAF A V+GG+ S+PGAV LL+G+ ES+ + + + +KD+ T+++L L+F P G Sbjct: 237 GVKAFVAMVMGGLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFFPQG 296 Query: 291 ILG 293 + G Sbjct: 297 LFG 299 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: 257 Number of extensions: 19 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: 305 Length adjustment: 27 Effective length of query: 273 Effective length of database: 278 Effective search space: 75894 Effective search space used: 75894 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