Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b21590 SM_b21590 inner membrane ABC transporter permease YjfF
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Smeli:SM_b21590 Length = 322 Score = 348 bits (892), Expect = e-100 Identities = 174/307 (56%), Positives = 228/307 (74%) Query: 4 RRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63 ++++PL T + + + + Q+ S RV+ NLL DNAFL I A+GMT VI+SGGID Sbjct: 3 QKYLPLTATILIFVLSYALCVAQYPNMLSTRVIGNLLTDNAFLGIAAVGMTFVILSGGID 62 Query: 64 LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123 LS+GAVIA +GV ++++ HPL+AF ++L + TLFGALMG IIH ++ FIVTLA Sbjct: 63 LSIGAVIAFAGVFLAVVLEHGGMHPLVAFALLLAITTLFGALMGAIIHYLEMPAFIVTLA 122 Query: 124 GMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHY 183 GMFLARG+A LS +SI I HPFY + + LPG G + L + + F + ++ H Sbjct: 123 GMFLARGMAFVLSIDSIPIKHPFYATLKSLYFKLPGGGRITLIGGLMLFVFAVGILIAHR 182 Query: 184 TRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIG 243 TRFGTN+YA+GG +A+LMG+ +A TTI IYA+S LA L+GIVF+ YT +GY+L A+G Sbjct: 183 TRFGTNIYALGGGTATAKLMGVPVAATTIRIYALSGLLAGLSGIVFSLYTSAGYSLAAVG 242 Query: 244 VELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLF 303 VELDAI AVVIGGTLLTGGSGFV GT++G+++ G+IQTYITFDG+LSSWWTKI+IGLLLF Sbjct: 243 VELDAITAVVIGGTLLTGGSGFVAGTLVGILIQGLIQTYITFDGTLSSWWTKILIGLLLF 302 Query: 304 FFILLQK 310 FILLQK Sbjct: 303 AFILLQK 309 Lambda K H 0.330 0.145 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: 474 Number of extensions: 27 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: 320 Length of database: 322 Length adjustment: 28 Effective length of query: 292 Effective length of database: 294 Effective search space: 85848 Effective search space used: 85848 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: 48 (23.1 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