Align TRAP-type large permease component (characterized, see rationale)
to candidate GFF4197 Psest_4270 TRAP transporter, DctM subunit
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__psRCH2:GFF4197 Length = 426 Score = 330 bits (845), Expect = 7e-95 Identities = 166/416 (39%), Positives = 265/416 (63%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 MT++ +L M IGVPVA SL G + + + + +A + ++ +TLLAIP Sbjct: 1 MTILFLFAALFVLMFIGVPVAVSLGLAGSLTIMIFSQDSVRSLAIKLFETSEHYTLLAIP 60 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAG M GG++RR+IDFA ACVGHIRGGL I A++A ++ A++SGS+ A AA+ + Sbjct: 61 FFLLAGAFMTTGGVARRLIDFANACVGHIRGGLAIGAVLACMLFAALSGSSPATVAAVGS 120 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 I I M ++GY AG++ G + +IPPS+ +V+ A S+ +LFMAG+VPG++ Sbjct: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSVVMVVYAAATETSVGKLFMAGVVPGIL 180 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 +G AL+ ++ K ++ LPR +E + A +A+W L + VIILGGI +G+ TPTEA Sbjct: 181 LGGALMIAIYIIAVKKNLPALPRASFREWLSAARKAIWGLLLMVIILGGIYSGMFTPTEA 240 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 A VAAVY+ FV + +Y+++ RD P V+L++ K + ++MF++ A++ + ++T IP Sbjct: 241 AAVAAVYSAFVALFVYKDISLRDCPKVLLESGKLSIMLMFIIANAMLFAHVLTTEQIPQA 300 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 IT ++ +P + + V+ +V+L+ G ++ + ILIL P+L PI Q GIDP++ G++ Sbjct: 301 ITAWVIEAGLQPWMFLLVVNIVLLIAGAFMEPSAIILILAPILFPIAIQLGIDPIHLGII 360 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 ++N IGL+TPPVG+ L V S V +P+ +VI V P+L + L ++ P I Sbjct: 361 MVVNMEIGLITPPVGLNLFVASAVTGMPVTQVIRAVLPWLALMLSFLVIITYVPSI 416 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: 485 Number of extensions: 14 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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