Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Dino:3607448 Length = 305 Score = 130 bits (328), Expect = 3e-35 Identities = 98/310 (31%), Positives = 152/310 (49%), Gaps = 32/310 (10%) Query: 5 VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGL 64 ++Q+LNGL G + L+A G T+V+G++G+IN AHG ++M+G FAA V S GL Sbjct: 7 IEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGATGSFVLGL 66 Query: 65 PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQG 124 A L A +L IE R L L ++ + + S + G Sbjct: 67 AAA------LAAAAAAGAL----IEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFG 116 Query: 125 --PRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 P +P +S FG + + II + A+ +FW ++ +T +G RA E Sbjct: 117 SFPLFLEVPAALSGPVTLPFGIEYPAYRLAIIGIGLAIAAALFW-LIAKTRIGVQIRAGE 175 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240 DR+M A LGV++D+ ++ F +GAALA +AG + V G + AF V+ Sbjct: 176 ADREMIAALGVDIDRLYTLVFALGAALAGLAGALVGALQSV-QVGMGEPVLILAFVVIVI 234 Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDV----------------ATFAILAFVL 284 GGIGS+ GA G LL+GL ++L +A+ V A + ++A VL Sbjct: 235 GGIGSIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAGVL 294 Query: 285 IFKPTGILGR 294 IF+P+G+ G+ Sbjct: 295 IFRPSGLFGQ 304 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: 294 Number of extensions: 25 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: 300 Length of database: 305 Length adjustment: 27 Effective length of query: 273 Effective length of database: 278 Effective search space: 75894 Effective search space used: 75894 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