Align Inner-membrane translocator (characterized, see rationale)
to candidate BPHYT_RS23885 BPHYT_RS23885 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__BFirm:BPHYT_RS23885 Length = 365 Score = 306 bits (785), Expect = 4e-88 Identities = 158/308 (51%), Positives = 213/308 (69%), Gaps = 1/308 (0%) Query: 5 RFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDL 64 R +P+ +T L +F G+ + GF S +V+ +LL DNAFLLI A+GMT VI+SGGIDL Sbjct: 15 RTLPIAVTILLFCALFGFGSVMYTGFFSWQVLLDLLVDNAFLLIVAIGMTFVIVSGGIDL 74 Query: 65 SVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAG 124 SVG+V+AL+ +V ++L W + +L +GT+FGA+ G +IH ++LQ FIVTLAG Sbjct: 75 SVGSVVALTTIVEAVLSEHLHWPVWVILPTVLLMGTVFGAVQGALIHFFRLQAFIVTLAG 134 Query: 125 MFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYT 184 MF ARGL ++ +SI I P + ++ + + G G++ + LI + + V H+T Sbjct: 135 MFFARGLCFLITTQSITITDPTFQKISAFRLDI-GVGSVTANVLIAFVTLLAAIYVAHFT 193 Query: 185 RFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGV 244 RFG NVYAIGGN SA LMG+ +A T I +YA+S F + L G VFTFY SGY L G+ Sbjct: 194 RFGRNVYAIGGNARSALLMGLPVAHTRIGVYALSGFCSALGGAVFTFYVLSGYGLQGQGM 253 Query: 245 ELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFF 304 ELDAIAA VIGGTLLTGG G+V+G++ GV ++G IQT ITFDG+LSSWWT+IVIG LL Sbjct: 254 ELDAIAATVIGGTLLTGGVGYVIGSLFGVGILGTIQTLITFDGTLSSWWTRIVIGALLCA 313 Query: 305 FILLQKLL 312 F LLQ+L+ Sbjct: 314 FCLLQRLI 321 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: 433 Number of extensions: 16 Number of successful extensions: 2 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: 365 Length adjustment: 29 Effective length of query: 291 Effective length of database: 336 Effective search space: 97776 Effective search space used: 97776 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: 49 (23.5 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