Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 210 bits (535), Expect = 3e-59 Identities = 112/308 (36%), Positives = 186/308 (60%), Gaps = 12/308 (3%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALM--MMG 65 F+Q +FN + GS YALIA+GYT+VYG++ +INFAHG+++M+G+Y++F + + L+ ++G Sbjct: 4 FIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGDLLG 63 Query: 66 IDT--GWLLVAAGFVGAIVIASAYGWSIERVAYRPVRN--SKRLIALISAIGMSIFLQNY 121 + GW +A +++ + G ++ER+AYRP+R + RL +I+A+ + L+N Sbjct: 64 VFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLILENG 123 Query: 122 VSLTEGSRDVALPSLFNGQ-WVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRM 180 G+ LP + + + G S S+T ++ + I FL L + +R+ Sbjct: 124 NLALLGASRRKLPDMVDKVVYTFG-----SVSVTNLKVWVIITAFLVFFLLQFIVTRTRI 178 Query: 181 GRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGM 240 G A RA A D L+GI D +I TFV+G+ A +AG+L Y +++PY+G M G Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238 Query: 241 KAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGIL 300 KAF AAV+GGIG I GA IGG +L E + +A+L + ++D+ +F +L+++L PTG+ Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLF 298 Query: 301 GRPEVEKV 308 G + K+ Sbjct: 299 GVAKTTKI 306 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: 244 Number of extensions: 8 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: 306 Length adjustment: 27 Effective length of query: 281 Effective length of database: 279 Effective search space: 78399 Effective search space used: 78399 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