Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate AZOBR_RS33690 AZOBR_RS33690 hypothetical protein
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__azobra:AZOBR_RS33690 Length = 500 Score = 424 bits (1089), Expect = e-123 Identities = 216/503 (42%), Positives = 329/503 (65%), Gaps = 4/503 (0%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 M+ LG L+ G +V+L+P NL+ GA +GTLIG LPGLGP VA+L+PL F L PP Sbjct: 1 MDLLGNLLLGLSVSLSPDNLLLCFGGALIGTLIGVLPGLGPTATVAMLLPLTFYL--PPV 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 A+I+L ++ G+ YGG ++IL+N+PG+ +++TCLDG+ MA++GRA ALA +A+AS Sbjct: 59 GALIMLAGIFYGSQYGGSATAILVNLPGESSSVVTCLDGHAMARQGRAGVALATAALASL 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 G++ TI + + P LA AL FGPAEY +L LL + + VK + LG++ Sbjct: 119 FAGIVTTILIAVAGPPLAGVALAFGPAEYVSLMLLGLIGAVTLAHGSVVKAIAMILLGLL 178 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGK 240 +S VG D+++G R+TFG+ +LY+GIDF+ +GLF ++E++ +E G G+ + Sbjct: 179 LSMVGTDVNSGDTRFTFGLPQLYDGIDFVPLAMGLFGLAEIISSLEQTGGAGQTTARIAS 238 Query: 241 LTLTMKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDIR 300 L +++ P +RG V+G + G+LPG GA+LGSF +Y+LEK+V +FG G I Sbjct: 239 LWPKREDVRQAWPATVRGTVMGALLGILPGGGATLGSFAAYSLEKKVSRHPERFGHGAIE 298 Query: 301 GVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGV 360 GV APEA NN AS +PML+LG+P + A+++ + ITPGP + + ++ WG+ Sbjct: 299 GVAAPEAANNAASQACFIPMLSLGIPPNAIMALMIGAMTIHGITPGPQIMAKQPELFWGM 358 Query: 361 IAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVA 420 IA++LIGNV+L++LN+P++G +V+LL VP YL P + + +G Y++++S F++ M Sbjct: 359 IASMLIGNVILVILNLPMIGLWVRLLRVPYGYLFPAILVFCCIGTYTLNNSGFNVLLMAL 418 Query: 421 FGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIVAG 480 FGV GY LRKL+ P++LG +LGP +E+NLG AL+LS G+ +V P++ L A Sbjct: 419 FGVLGYALRKLDCEPAPLMLGFVLGPMLEENLGRALLLSGGDPTVFATRPISGSLLATAA 478 Query: 481 LGLILPYLVGPLLRRRMNAAMKE 503 L LIL +V P +RRR + A K+ Sbjct: 479 LLLIL--MVMPSVRRRRDEAFKD 499 Lambda K H 0.325 0.144 0.425 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: 709 Number of extensions: 35 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: 508 Length of database: 500 Length adjustment: 34 Effective length of query: 474 Effective length of database: 466 Effective search space: 220884 Effective search space used: 220884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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