Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate SM_b20027 SM_b20027 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Smeli:SM_b20027 Length = 501 Score = 402 bits (1034), Expect = e-116 Identities = 200/485 (41%), Positives = 318/485 (65%), Gaps = 2/485 (0%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 M+ + L+ GFA A +P NL+ LIG +GT++G+LPG+G +A+LLP+ F L Sbjct: 1 MELFSNLALGFATAASPANLLFCLIGVLLGTLIGVLPGIGATATIAMLLPITFQLE--PV 58 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 S+LI+LA +Y G +YGG ++IL+N+PG++++ +TA+DGY MA++G+ G AL+I+A+ SF Sbjct: 59 SSLIMLAGIYYGAQYGGSTTAILINMPGESSSAVTAIDGYQMARKGRAGTALAIAALGSF 118 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 F ++ + LFAP L + +L FG AEYF+LM+ + ++ + +K+ +GL Sbjct: 119 FAGTVSTFLVALFAPPLTEIALEFGAAEYFSLMIVGLVSSVALAHGSVIKALAMVALGLL 178 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240 L VG D TG RFT SDG+ F+ + +G+F ++EIL LE + + ++ K Sbjct: 179 LGLVGTDIYTGTPRFTLGIREYSDGLNFVALAVGVFGIAEILRNLESEKTREVLMAKVTD 238 Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300 ++ ++ Q + LR + IG +GVLPG GA +A+ +Y EK+LS + FG+G + Sbjct: 239 LMPTREDFRQMVAPVLRGTAIGSALGVLPGGGAILAAFASYTVEKRLSDRPEEFGRGAVA 298 Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360 GVA PE+ANNA A SFIP+LTLG+P + A+M+GA+ + I PGP + EQP + WG+ Sbjct: 299 GVAGPESANNAGAQTSFIPLLTLGIPANPVMALMIGAMIIQGIVPGPNVAVEQPALFWGI 358 Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420 IA++ I N+ML+++N+PLIGL+ ++L IP + + P I A ++GVY+V+S +DL + Sbjct: 359 IASMWIGNLMLVVLNLPLIGLWVKLLKIPYFVLFPIIMAFCSIGVYSVNSNVYDLYAVAF 418 Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAI 480 G++GY+L K+ +PL+LGFVLG +LE+NLRRA+ +S G+ ++ LL++A+ Sbjct: 419 FGLVGYLLLKLRCEPAPLLLGFVLGPLLEENLRRAMILSRGDPTTFVTRPISATLLLIAL 478 Query: 481 MVIVV 485 V+VV Sbjct: 479 AVLVV 483 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: 747 Number of extensions: 38 Number of successful extensions: 3 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: 501 Length adjustment: 34 Effective length of query: 470 Effective length of database: 467 Effective search space: 219490 Effective search space used: 219490 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