Align Tricarboxylate transport protein TctC (characterized)
to candidate 3607812 Dshi_1220 hypothetical protein (RefSeq)
Query= reanno::Dino:3609740 (326 letters) >FitnessBrowser__Dino:3607812 Length = 328 Score = 115 bits (289), Expect = 1e-30 Identities = 99/331 (29%), Positives = 147/331 (44%), Gaps = 13/331 (3%) Query: 1 MTLEFTRRTL--IAAAAALAMTGGAHAEGE-QMLESIHFLIPGGAGGGWDGTARGTGEAL 57 MTL FTRR IA AAA ++ A A+ + + + I +I G GGG D AR + Sbjct: 1 MTLNFTRRVALTIATAAATSIALPAFADDDWKPNKPIEMVIMAGQGGGADRLARLFQSII 60 Query: 58 TKAGLVGSASYE-NMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRD 116 K L N GG G +A+ YL + SH +M + +I + Sbjct: 61 QKENLASMPVLPVNKGGGSGAEALRYLKDKEGDSH-VIMATLNSYYTTPIRTDIGVDIEE 119 Query: 117 LTLVAGTIGDYAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVME 176 T +A D + V DS I ++ D +AA +A A +GG G D LV AM+ + Sbjct: 120 FTPLARMALDTFVLWVNADSDIYTLEDYVAAVNASGGAWKMGGTGT-GQEDSLVTAMLEK 178 Query: 177 AAGKDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVA 236 G + Y+P++ GG L+ G I + SEA+ +AG+V+ I PER+A Sbjct: 179 EFG---IKHTYVPFNGGGTVAKNLVGGHIDSTVNNPSEAMGFWQAGKVRPIAAFTPERLA 235 Query: 237 AYDSAPTMVEQGIDTTFVNW--RGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNG 294 + PT E G + + V W R F +P E +A Y A E + T EW+ Sbjct: 236 VFPDVPTATELGHE-SLVYWMQRSFVGPKDMPAEAVAYYTAMFEGLAQTEEWQTYTQEKA 294 Query: 295 WVNIHNSGADFQS-FLEAQEAQIGDLMKKLG 324 + +G Q+ FLE ++ L + G Sbjct: 295 LMADFLTGDALQAYFLEERDKHAAILQEMEG 325 Lambda K H 0.315 0.132 0.378 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: 298 Number of extensions: 18 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: 326 Length of database: 328 Length adjustment: 28 Effective length of query: 298 Effective length of database: 300 Effective search space: 89400 Effective search space used: 89400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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