Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate HSERO_RS13470 HSERO_RS13470 C4-dicarboxylate ABC transporter
Query= reanno::SB2B:6938090 (466 letters) >FitnessBrowser__HerbieS:HSERO_RS13470 Length = 449 Score = 224 bits (572), Expect = 3e-63 Identities = 158/477 (33%), Positives = 243/477 (50%), Gaps = 53/477 (11%) Query: 1 MTIATLF-LTLFLCMLLGMPIAIALGFSSMLTILLFSNDS-LASVALKLYEATSEHYTLL 58 +T+ L+ + + M GMPIA ALG + + F +S L ++ +YE + TLL Sbjct: 4 LTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIAS-ITLL 62 Query: 59 AIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAA 118 +IP FIL A + + + + + GGL +A+V AC LFAA++GSSPAT +A Sbjct: 63 SIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSA 122 Query: 119 IGSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIP 178 IGS I M R GY FAAG+I GTLGIL+PPSI M++YA A E S R+F+AG+ P Sbjct: 123 IGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGP 182 Query: 179 GLLMGVLLM-VAIYIVARIKNLPSRPFP--GVKALSLSS------------AKAMGGLAL 223 G+L+ +L A+Y + L + G K+ L + + L L Sbjct: 183 GVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLIL 242 Query: 224 IFIVLGSIYGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNL 283 + V+ ++YGG+A+P+E A + + A ++ YR P Sbjct: 243 LIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKP--------------------- 281 Query: 284 LHVGLGLIKTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGW 343 +EI + K S MLL II ++L+++V++ I A+ +V Sbjct: 282 -------------REIAPFLSSTIKESGMLLLIIGMSLLYSYVMSYLHISQSAAQWVVDL 328 Query: 344 GLPPWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIG 403 L W L ++ +++ G F+ P +I+L+ API+ P G D I GI+M V ME+G Sbjct: 329 HLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDLIWFGIVMTVVMEMG 388 Query: 404 MLTPPVGLNLFVTAGIT-GRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459 ++ PPVGLNLFV I ++G VI +P+L L+ ++L+ P I+ LP+ L Sbjct: 389 LIHPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVLLLCMFPGIATLLPDLL 445 Score = 26.9 bits (58), Expect = 0.001 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 1/43 (2%) Query: 112 SPATVAAIGSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPS 154 SP T+ + +V + ++ +G P FA GV+ T G + +P S Sbjct: 2 SPLTLGVLYGVVTIVVMCSGMPIAFALGVVAT-GFMYFFMPES 43 Lambda K H 0.329 0.144 0.424 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: 653 Number of extensions: 44 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 466 Length of database: 449 Length adjustment: 33 Effective length of query: 433 Effective length of database: 416 Effective search space: 180128 Effective search space used: 180128 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 (21.8 bits) S2: 51 (24.3 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