Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1939 Length = 291 Score = 160 bits (405), Expect = 3e-44 Identities = 102/300 (34%), Positives = 163/300 (54%), Gaps = 14/300 (4%) Query: 4 FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63 FVQ L++G++ G IYGL+A+G+ ++Y ++FA G++ MLG F L + VL G Sbjct: 3 FVQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVL-----G 57 Query: 64 LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123 P V +L VVAM L+ +ER RP+ G + ++ IG+ L + + Sbjct: 58 FPFWVAVLAS-VVAM---GLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMIP 113 Query: 124 --GPRNKPIP-PMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 G +P P + G + VS +Q+++I T L + + + + LG A +A Sbjct: 114 NIGTDTHTLPVPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQAAS 173 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240 Q++ A +G+ V + + + + A +AAVAG + V + N GF G+KAF AAV+ Sbjct: 174 QNQLAAYYMGIPVQRLNGLAWGLAAVVAAVAGLLLAPITFVHA-NMGFI-GLKAFPAAVV 231 Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300 GG GSLPGA+ GGL+IG++ESL Y +KD A + ++ +L+ KP G+ G +KV Sbjct: 232 GGFGSLPGAIVGGLVIGIVESLSGFYLPDGFKDTAAYIVVLIMLMVKPNGLFGEKLRKKV 291 Lambda K H 0.329 0.143 0.421 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: 277 Number of extensions: 21 Number of successful extensions: 5 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: 300 Length of database: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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