Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate PfGW456L13_3701 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
Query= TCDB::O50183 (232 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3701 Length = 232 Score = 398 bits (1022), Expect = e-116 Identities = 195/231 (84%), Positives = 222/231 (96%) Query: 1 MIFDFSVIWDSLPLYFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTY 60 MI D+++IW++LPLYF+G L+TLK+L ISL +GL+LA+PLALMRVS+ PL+NFPAWLYTY Sbjct: 1 MILDYNLIWENLPLYFNGALLTLKVLLISLALGLVLAIPLALMRVSRSPLINFPAWLYTY 60 Query: 61 VIRGTPMLVQLFLIYYGLAQFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSL 120 VIRGTPMLVQLFLIYYGLAQF+AVR+SALWP+LS+A+FCACLAFAINTSAY+AE+LAGSL Sbjct: 61 VIRGTPMLVQLFLIYYGLAQFEAVRQSALWPYLSSATFCACLAFAINTSAYSAELLAGSL 120 Query: 121 KATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDI 180 K+TPHGEIEAA+AMGMSRL +YRRIL+PSALRRALPQYSNEV+MMLQTTSLASIVTLVDI Sbjct: 121 KSTPHGEIEAARAMGMSRLTLYRRILMPSALRRALPQYSNEVLMMLQTTSLASIVTLVDI 180 Query: 181 TGAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERRWLAYLAPRK 231 TGAARTV S++YLPFEAFITAGLFYL LTFILVRLFKLAER WLAYLAPRK Sbjct: 181 TGAARTVSSRFYLPFEAFITAGLFYLALTFILVRLFKLAERHWLAYLAPRK 231 Lambda K H 0.330 0.140 0.425 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: 237 Number of extensions: 1 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: 232 Length of database: 232 Length adjustment: 23 Effective length of query: 209 Effective length of database: 209 Effective search space: 43681 Effective search space used: 43681 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 (21.9 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