Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO356_29015 AO356_29015 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29015 Length = 293 Score = 124 bits (310), Expect = 3e-33 Identities = 91/306 (29%), Positives = 156/306 (50%), Gaps = 19/306 (6%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAAL-IVFLVLTS 59 M +F++ L+ GL G++Y LVAIG+ ++Y G+ NFA G + + FAAL V L Sbjct: 1 MNFFLETLIGGLLAGTLYSLVAIGFVLIYKASGVFNFAQGAMLL---FAALTFVSLREQG 57 Query: 60 IFAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFI 119 + L + + +LVM+V A+L IER+ RPL ++ + +G+S + Sbjct: 58 LSFALALLLTVLVMVVGALL--------IERLVLRPLVNRSQITLFMATLGLSFIIEGLA 109 Query: 120 QVTQGPRNKPIPPMVSSVYQF-GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178 Q G + + + + V F G I +S +I ++A+ + + + N+T +G A RA Sbjct: 110 QGLMGAQVRALDLGIEDVPLFVGEIMISQFDLIAAGVSALTVAVLALLFNKTRIGVALRA 169 Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238 D + A LG+N+++ I + + + VAG ++ GV F+ +KA Sbjct: 170 VADDTRAALSLGINLNRIWQIVWAVAGVVGLVAGLLWGARQGV-QFSLSLVV-LKALPVL 227 Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYF--TIAYKDVATFA-ILAFVLIF-KPTGILGR 294 ++GG S+ GA+ GGL++G E+L AY I FA LA + ++ +P G+ G Sbjct: 228 IIGGFTSIGGAIVGGLIVGAAENLAEAYIGPLIGGGITPWFAYFLALIFLYIRPAGLFGD 287 Query: 295 PEVEKV 300 +E+V Sbjct: 288 RIIERV 293 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: 293 Number of extensions: 26 Number of successful extensions: 5 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: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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