Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate SMc00500 SMc00500 hypothetical protein
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Smeli:SMc00500 Length = 505 Score = 342 bits (878), Expect = 1e-98 Identities = 183/488 (37%), Positives = 290/488 (59%), Gaps = 4/488 (0%) Query: 9 QGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILLAT 68 Q V + + + + G +G ++G LPGLGP G+++L+P F +L E +++L+ + Sbjct: 6 QSLGVIFSLSGVAVLVTGALLGIVIGALPGLGPSIGLSLLIP--FTYNLGPELSMLLMIS 63 Query: 69 VYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIAIG 128 +Y EYGG IS+ILL+ PG AAA TA+DGY MA+QGK A+SIS +S G ++ Sbjct: 64 LYTSAEYGGSISAILLSTPGTAAAAATAIDGYSMARQGKANEAISISLTASTVGGVLGGL 123 Query: 129 GIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGVDA 188 ++L A LA +L FGPA YFA+ VF ++ + ++ + +K A GL LATVG+D Sbjct: 124 ALLLLAMPLASLALKFGPAGYFAVGVFGLSSVAALSGGSLVKGLACAAFGLALATVGIDP 183 Query: 189 NTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLE-HTSSGQTMVRKTGRMLFNLKE 247 G RFTF L +GV F+ +IGLF+VSE L M+E S ++ K G + + Sbjct: 184 IAGTPRFTFGLFQLYEGVPFLAALIGLFAVSEALAMVESRVVSAPSIKDKVGHVFMSAAL 243 Query: 248 GAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIRGVAAPEA 307 + + L SVIG +G+LPG G IA + + + + FG G G+AAPEA Sbjct: 244 WKETWHSMLSGSVIGTLLGILPGVGGNIACWVARDYARARDRHPEEFGNGSANGIAAPEA 303 Query: 308 ANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGLIAALLIA 367 ANNA+ G+ +P+L LGVPGS TTA+M+GAL ++ + PGP +F E P +V+ ++ +IA Sbjct: 304 ANNATVGGALVPLLALGVPGSPTTAIMVGALIMHGLHPGPQLFNEAPSLVYAILFGTIIA 363 Query: 368 NVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVALGVLGYI 427 +++ + L R++ +P + I A + +G +A+ + FD+ LM+ GV+GY+ Sbjct: 364 SLVQYAAGSLFLPLMARVMRLPDAVIAVGIMAFAVLGAFAIRNLMFDVYLMLGFGVVGYL 423 Query: 428 LRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAIMVIVVPP 487 ++K+ FP++P+IL VLG ++E N R AL S G+ I ++ LI++ +V ++ P Sbjct: 424 MKKLRFPVAPVILAMVLGYLVESNYRTALVSSQGDYTIFVTDPISLIFLILS-LVSLLTP 482 Query: 488 VLRLLRKH 495 + R ++ H Sbjct: 483 LWRRIQAH 490 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: 725 Number of extensions: 44 Number of successful extensions: 6 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: 505 Length adjustment: 34 Effective length of query: 470 Effective length of database: 471 Effective search space: 221370 Effective search space used: 221370 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