Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 3609311 Dshi_2696 inner-membrane translocator (RefSeq)
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__Dino:3609311 Length = 554 Score = 130 bits (328), Expect = 5e-35 Identities = 98/304 (32%), Positives = 156/304 (51%), Gaps = 17/304 (5%) Query: 2 SEQFLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMI--IA 59 +++F Q ++ G++LGS L AIG + +G++G+IN AHGE+ MIG+Y +F + I Sbjct: 252 NQRFWNMAQNVWFGLSLGSVLLLAAIGLAITFGVMGVINMAHGELVMIGAYTTFFVQEII 311 Query: 60 ALMMMGIDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQ 119 + LL+AA A +A A G +IER R + L L++ G+S+ LQ Sbjct: 312 RTSFPHLFDWSLLIAAPL--AFAVAGAVGVAIERGCVR-FLYGRPLETLLATWGISLILQ 368 Query: 120 NYVSLTEG--SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTF-LAMLALTIFI- 175 V G +R+V PS +G + VG +T +WI+ F LA+ A+ +F+ Sbjct: 369 QTVRSIFGPNNREVGNPSWMSGAFEVG-------QMTITYNRLWILLFALAVFAVLLFVL 421 Query: 176 RYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIG 235 + + +G RA ++ MA+ +GI T V A+TF +GA +A +AGV L Q V +P +G Sbjct: 422 KKTAIGLQMRAVTQNRAMAANMGIRTGWVDAMTFGLGAGIAGLAGVALSQIDNV-SPNLG 480 Query: 236 FMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVM 295 + +F V GG G+I G + LGIA Y ++ +IL + Sbjct: 481 QSYIVDSFMVVVFGGAGNIWGTLAAAFSLGIANKFLEPYAGAVLAKILVLVFIILFIQKR 540 Query: 296 PTGI 299 P G+ Sbjct: 541 PRGL 544 Lambda K H 0.328 0.141 0.410 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: 295 Number of extensions: 9 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: 308 Length of database: 554 Length adjustment: 31 Effective length of query: 277 Effective length of database: 523 Effective search space: 144871 Effective search space used: 144871 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: 50 (23.9 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