Align TRAP-type large permease component (characterized, see rationale)
to candidate GFF3396 PS417_17380 membrane protein
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__WCS417:GFF3396 Length = 426 Score = 303 bits (775), Expect = 9e-87 Identities = 159/416 (38%), Positives = 258/416 (62%), Gaps = 3/416 (0%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 M ++ + S + + IG+PVA++L ++ W++ + ++ Q + G + F+L+AIP Sbjct: 1 MDALILLGSFIALILIGMPVAYALGLSALIGAWWIDIPFQALMIQ-VAGGVNKFSLMAIP 59 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAG +M GG+SRR++ FA VG +RGGL +V IMA+ +ISGS+ ADTA++ + Sbjct: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAA--NVSITQLFMAGIVPG 178 +LIP M + GY + + +G V A + PPS +++ +AA +VSI LFMAG+VPG Sbjct: 120 VLIPEMERRGYPREFATAVTVSGSVQALLTPPSHNSVLYSLAAGGSVSIASLFMAGVVPG 179 Query: 179 LIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPT 238 L+M L+ L+ +K + P+K+ + ALW L VIILGGI +G+ T T Sbjct: 180 LLMSACLMVLCLIFAKKRNYPKGEVIPLKQALKICADALWGLMAMVIILGGILSGIFTAT 239 Query: 239 EAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIP 298 E+A +A ++A FV M IYR+ K +LP ++ + +T +++M L+ A +++T IP Sbjct: 240 ESAAIAVLWAFFVTMFIYRDYKWSELPKLMHRTVRTISIVMILIAFAASFGYIMTLMQIP 299 Query: 299 SEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFG 358 ++IT L D +++ I ++L++GT +D+ P ILILTP+L+P++ G+DPV+FG Sbjct: 300 AKITTLFLTLSDNRYVILMCINAMLLLLGTVMDMAPLILILTPILLPVVLGIGVDPVHFG 359 Query: 359 VLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFP 414 ++ ++N IGL+TPPVG VL V + VG+V + K + + PF LVL + P Sbjct: 360 MIMLVNLGIGLITPPVGAVLFVGAAVGKVSIEKTVKALLPFYGVLFLVLMAVTYIP 415 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: 463 Number of extensions: 22 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: 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