Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= CharProtDB::CH_011913 (426 letters) >MicrobesOnline__882:206177 Length = 596 Score = 98.6 bits (244), Expect = 5e-25 Identities = 57/140 (40%), Positives = 86/140 (61%), Gaps = 5/140 (3%) Query: 284 FTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVI 343 FTG F+ F I L++YT+AF+AE++RAG+Q+I +G EAAY+ GL + + +I Sbjct: 133 FTGNFE----FWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLNYVQVLRTII 188 Query: 344 LPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIY 403 LP A R I+PPL S+FLN KNSSLA+ V +L + + T + E ++Y Sbjct: 189 LPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWQSQQVE-SLTFKGFEATSAATVLY 247 Query: 404 LTISLTISSLMNLYNKSIKL 423 L++SL IS ++N N ++L Sbjct: 248 LSLSLLISFILNGVNGKMRL 267 Score = 85.5 bits (210), Expect = 4e-21 Identities = 44/91 (48%), Positives = 63/91 (69%) Query: 294 FTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVP 353 F + IALTL+T A++AEIVRAGIQ I GQ EAAY+ GL +TM +ILPQAL+ ++P Sbjct: 460 FWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIP 519 Query: 354 PLISQFLNLTKNSSLAIAVSYMDLRGTLGGI 384 ++ QF+ + K++SLA + ++L GI Sbjct: 520 AIVGQFIAIFKDTSLAFVLGVLELTFVAQGI 550 Score = 42.0 bits (97), Expect = 5e-08 Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 18/105 (17%) Query: 57 DFNFSFLWTRAGYDLAQTLIPYSNDDTHFRAL----IEGLLNTLLVSVLGCILATILGTI 112 DF + F W I ++ + T+ L ++GL T+ +S++ LA LGT+ Sbjct: 32 DFGYQFQWD----------ILFTRNTTYGTHLGLEILKGLGVTVRISLISSALALGLGTV 81 Query: 113 IGVLRLSQNWLVARIMTVYVETFRNIPLLL----WILLMGTILAE 153 +G+ RLS + T VE FRN PLL+ W IL E Sbjct: 82 LGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFAFPAILPE 126 Score = 37.7 bits (86), Expect = 1e-06 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 7/101 (6%) Query: 60 FSFLWTRAGYDLAQTLI---PYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVL 116 ++F W +L LI P D F L GL +LL++V+ ++ +G ++G+ Sbjct: 356 YNFNWGVIADNLRTLLIWHFPNGQSDELFMGL-GGLAYSLLMAVIAISVSFFIGLVVGIG 414 Query: 117 RLSQNWLVARIMTVYVETFRNIPLLL---WILLMGTILAET 154 R S N + +Y+E R PL++ WI +L T Sbjct: 415 RTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLFNT 455 Lambda K H 0.326 0.139 0.419 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: 530 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 4 Length of query: 426 Length of database: 596 Length adjustment: 34 Effective length of query: 392 Effective length of database: 562 Effective search space: 220304 Effective search space used: 220304 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 (21.7 bits) S2: 52 (24.6 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