Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_012116029.1 XAUT_RS20525 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000017645.1:WP_012116029.1 Length = 291 Score = 171 bits (432), Expect = 2e-47 Identities = 96/303 (31%), Positives = 174/303 (57%), Gaps = 19/303 (6%) Query: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDT 68 +Q + +G+ +G YAL+A+G+ +++ +NFAHG+ MIG ++ ++AA + +G+ Sbjct: 5 VQYILSGLAIGGIYALVALGFHIMWSSAKAVNFAHGDTLMIGGLLAVYLLAAGLPLGL-- 62 Query: 69 GWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIA-LISAIGMSIFLQNYVSL-TE 126 + A+V +G +ER+A RP + + + +++ I + I ++++ ++ T+ Sbjct: 63 -------ACLAAVVAGGLFGLVLERIAVRPFLSQQGSVGWMLTTIAVGIMVESFATIQTQ 115 Query: 127 G-SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185 G +R + P + + ++G A I + VI +V +AML L R++ +GRA R Sbjct: 116 GYARPLPSPGVASSVHILG------AGIYPQELVIPLVAVVAMLGLRALQRHTLVGRAMR 169 Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245 A A + A+L+GIN + V+A +F + + A AGVL+ + +G + G+K F Sbjct: 170 AVAHNKNAAALMGINVNAVVAFSFALAGLLGAAAGVLVAPVVQA-SAAMGVLPGLKGFAV 228 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEV 305 A++GGI S PG +I GL+ G+ E Y+ST ++++ F+L+IL LLV P G+ G+ EV Sbjct: 229 AIIGGITSAPGVVITGLVYGVMEKFVEGYISTAAREIIGFSLMILTLLVFPQGLFGKREV 288 Query: 306 EKV 308 KV Sbjct: 289 MKV 291 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: 243 Number of extensions: 11 Number of successful extensions: 4 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: 291 Length adjustment: 27 Effective length of query: 281 Effective length of database: 264 Effective search space: 74184 Effective search space used: 74184 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 24 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