Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011383887.1 AMB_RS07460 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000009985.1:WP_011383887.1 Length = 618 Score = 132 bits (333), Expect = 2e-35 Identities = 89/299 (29%), Positives = 146/299 (48%), Gaps = 9/299 (3%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M +F Q LNGL S LVA G ++++G+ ++NFAHG +MLG + A F ++ + Sbjct: 1 MSFFFIQFLNGLASASSLFLVASGLSIIFGVSRIVNFAHGSFYMLGAYMA---FTLVQKL 57 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 G ++L A + +L +E V R + + L L+ G+ + + + + Sbjct: 58 SGGTVFGFWGAIVLAAAAV--ALVGAVVEMVLLRRIYQAPELLQLLATFGLVLIVQDLVL 115 Query: 121 VTQGPRNK--PIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178 V GP + P P + S ++I++ V+L + W + +RT G RA Sbjct: 116 VLWGPEDLLGPRAPGLKGAIDIFGQSFPQYDFVLIILGPVVLGLLWLLFHRTRWGTLIRA 175 Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238 QDR+M A LGVN + F +GA LA + G + L V D +AF Sbjct: 176 ATQDREMVAALGVNQAWLFTSVFTLGAFLAGLGGAVQLPREAVNHVMD-LQIITEAFVIV 234 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297 V+GG+GS+ GA ++IG + + F V TF ++A +L+ +P G+LG+PE+ Sbjct: 235 VIGGLGSVLGAFLAAVIIGELNAFGILIFP-QLTLVLTFLVMAVILVVRPWGLLGKPEM 292 Score = 56.2 bits (134), Expect = 2e-12 Identities = 67/288 (23%), Positives = 115/288 (39%), Gaps = 23/288 (7%) Query: 11 GLTLGS---IYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLPVA 67 GL++ S I+ L A + G GM++F H F LG + A ++ + G+P+ Sbjct: 333 GLSVASEVLIFALFAASLHFMMGTGGMVSFGHAAYFGLGSYGAALMVK-----YFGIPML 387 Query: 68 VLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGPRN 127 L+ ++A ++ W R+A L LA A + S+F G Sbjct: 388 AALVTGPLLAAAAALVFGWFCVRLAGAYL-AMLTLAFAQIAYAVVFQWSSFTGGDNGLIG 446 Query: 128 KPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDRKMAA 187 P ++ F ++++L I+ + + F Y + RA A Sbjct: 447 IWPAPWAANPVAFYYLTLALCGGGILAVRRITFAPFGYTL---------RACRDSALRAD 497 Query: 188 LLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFND--GFTPGVKAFTAAVLGGIGS 245 +G+N+ F + A +AG++Y G + F D V +LGG+ + Sbjct: 498 SIGINLSSHRWAGFALAGFFAGIAGSLYAFLKG-SVFPDTISIATSVDGLVMVLLGGVQT 556 Query: 246 LPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILG 293 L G V G L+ + S+Y T ++ I+ V+ F P GI G Sbjct: 557 LTGPVVGALVYKTLHVTISSY-TDQWRTALGVIIIVLVVAF-PQGISG 602 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: 613 Number of extensions: 39 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 300 Length of database: 618 Length adjustment: 32 Effective length of query: 268 Effective length of database: 586 Effective search space: 157048 Effective search space used: 157048 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: 51 (24.3 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