Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 193 bits (491), Expect = 4e-54 Identities = 110/292 (37%), Positives = 175/292 (59%), Gaps = 14/292 (4%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 FLQQ+ NG+TLG Y+L+A+G T+VYGI+ + NFAHG YM G+YVS+ ++ +L M Sbjct: 4 FLQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVSYYLMTSLGM---- 59 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 WL + A + V++ +R+ + P+RN+ L +I+AIG+ +FL+ G Sbjct: 60 NYWLAMGAAAIAVAVLSML----ADRLVFHPLRNAPELHDMIAAIGIMLFLEAGAQAMWG 115 Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187 + +P+ + GQ V E S + +I F M+ L +F+ + G A Sbjct: 116 ADFHRMPTPY-GQMV----EVMGLSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAM 170 Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247 A++ + A+L+GI+ RV L F I A+AA+A L ++ P +G + KAF + Sbjct: 171 AQNREGAALVGIDATRVTLLVFAISGALAAIAATLYAPI-NLVYPSMGNLVITKAFVIII 229 Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGI 299 LGG+GSIPGA++GGLI+G+AE+ Y+ST+YKD+++FALL+L+L + P G+ Sbjct: 230 LGGMGSIPGAIVGGLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGL 281 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: 232 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: 287 Length adjustment: 26 Effective length of query: 282 Effective length of database: 261 Effective search space: 73602 Effective search space used: 73602 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