Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate AZOBR_RS25235 AZOBR_RS25235 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__azobra:AZOBR_RS25235 Length = 499 Score = 409 bits (1051), Expect = e-118 Identities = 204/493 (41%), Positives = 320/493 (64%), Gaps = 5/493 (1%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 MD+ ++ G ++A +P NL+ G +GT VG+LPG+GP+ +A+LLP F+L Sbjct: 1 MDSLGGIAHGLSIAASPANLLYCFAGALLGTFVGVLPGVGPLLTIALLLPFTFSLE--PT 58 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 ALI+LA +Y G +YGG +SILLN+PG+ ++++T +DG+ MA+QG+GG AL+++A+ SF Sbjct: 59 GALIMLAGIYYGAQYGGSTTSILLNMPGETSSVVTCIDGHAMARQGRGGPALAVAAIGSF 118 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 ++ G + FAP+LA ++ FGPA+YF+LMV + + + +K+ ++GL Sbjct: 119 IAGTLSTGIVAFFAPVLAGVAIRFGPADYFSLMVLGLVGAIVLAQGSFVKALAMIVLGLL 178 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240 VG D N+G R TF L+DG+ F+ V +G+F + EI+ +L V G Sbjct: 179 FGLVGTDVNSGEQRLTFGIQALADGIGFVPVALGVFGIGEIIRILIGQERDGGQVIPHGS 238 Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300 ++ + ++ G R SVIG +G+LPG GA +A+ +Y EKKL+ + FG+G I Sbjct: 239 LMPSRQDLRDSSGAIARGSVIGSALGLLPGGGAALAAFASYTVEKKLARDPSRFGRGAIE 298 Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360 GVA PE+ANNA+A SFIP+LTLG+P + A+M+GAL L+ ITPGP + +PD+ WG+ Sbjct: 299 GVAGPESANNAAAQTSFIPLLTLGLPSNAVMALMIGALMLHGITPGPRIMQAEPDLFWGV 358 Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420 +A++ I N ML+++N+PL+GL+ R+L +P F+ P I VS VGVY V ++ FDLV Sbjct: 359 VASMWIGNAMLIVLNLPLVGLWVRLLRVPYRFLYPTIVLVSCVGVYGVSNSAFDLVTTAV 418 Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMA- 479 G+LG++L+ + F +PL+LGFVLG M+E+NLRRA+ +S G+ + + ++ ALL++ Sbjct: 419 FGLLGWVLQALRFEPAPLLLGFVLGPMMEENLRRAMILSRGDPTVFLREPISLALLVLTG 478 Query: 480 --IMVIVVPPVLR 490 + I++P V R Sbjct: 479 VLLAAIILPTVRR 491 Lambda K H 0.326 0.141 0.414 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: 763 Number of extensions: 29 Number of successful extensions: 7 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: 504 Length of database: 499 Length adjustment: 34 Effective length of query: 470 Effective length of database: 465 Effective search space: 218550 Effective search space used: 218550 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 (21.6 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