Align TRAP-type large permease component (characterized, see rationale)
to candidate 202250 SO3136 C4-dicarboxylate transport protein (NCBI ptt file)
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__MR1:202250 Length = 465 Score = 271 bits (693), Expect = 3e-77 Identities = 147/451 (32%), Positives = 254/451 (56%), Gaps = 35/451 (7%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMI-AGADTFTLLAI 59 M + L M +G+P+A +L F ++ + + + +A + + ++ +TLLAI Sbjct: 1 MAIATLFCVLFICMFLGMPIAIALGFSSMLTILFFSNDSLASVALKLYESSSEHYTLLAI 60 Query: 60 PFFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALA 119 PFFIL+ ++ GG++RRIIDFA+ CVGHIRGGL + ++MA ++ A++SGS+ A AA+ Sbjct: 61 PFFILSSAFLSTGGVARRIIDFAMDCVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 Query: 120 AILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGL 179 +I+I M KAGY ++G+I G + +IPPS+ +V+ A VS+ ++FMAG+VPGL Sbjct: 121 SIVIVGMVKAGYPEKFASGVITTSGTLGILIPPSIVMLVYAAATEVSVAKIFMAGLVPGL 180 Query: 180 IMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTE 239 ++G ++ +V R ++ +P K+ ++ +A+ L + I+LG I GV +PTE Sbjct: 181 LLGFLIMVVIYIVARIKNLPSIPFPGFKKLGVSSAKAIGGLALIFIVLGSIYGGVASPTE 240 Query: 240 AAVVAAVYALFVGMVIYRELKP----------------------------------RDLP 265 A+ VA VYA F+ + YR++ P +++ Sbjct: 241 ASAVACVYAYFIAVFGYRDIGPLKNVAWRNPNEAIPSAIARNLGHMVLGLIKTPIDKEIR 300 Query: 266 GVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLIDRPTLLMFVIMLVVLV 325 V+ AK + +++F++ A++ + ++T IP I +I + + ++ L++L Sbjct: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEYIVGMGLPAWGFLIIVNLLLLA 360 Query: 326 VGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGLLTPPVGVVLNVVSGVG 385 G ++ + +LI+ P+L PI Q GIDP++ G++ ++N IG+LTPPVG+ L V SG+ Sbjct: 361 AGNFMEPSAIVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTSGIT 420 Query: 386 RVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 +G VI V P+LV + L L+ P I Sbjct: 421 GRNIGWVIQSVLPWLVFMLAFLMLITYVPQI 451 Lambda K H 0.331 0.145 0.430 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: 481 Number of extensions: 18 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: 425 Length of database: 465 Length adjustment: 32 Effective length of query: 393 Effective length of database: 433 Effective search space: 170169 Effective search space used: 170169 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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