Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_005457271.1 SACCYDRAFT_RS14745 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >NCBI__GCF_000244975.1:WP_005457271.1 Length = 369 Score = 130 bits (326), Expect = 6e-35 Identities = 102/314 (32%), Positives = 165/314 (52%), Gaps = 20/314 (6%) Query: 8 PLWITASLLLTMFLVGTFQFD-----GFASGRVVTNLLRDNAFLLITALGMTLVIISGGI 62 P+ A+LL+ +V FD G G ++ ++L++ A L+ ALGMTLVI + GI Sbjct: 20 PVLALAALLVVNVVVTPSFFDIRLQDGHLYGSLI-DILKNGAPTLLIALGMTLVIATRGI 78 Query: 63 DLSVGAVIALSGVVTSLLITEYQ-----WHPLLAFVVILPLGTLFGALMGTIIHVYKLQP 117 DLSVGAV+A++G V I LA + L L L GA G ++ V +QP Sbjct: 79 DLSVGAVVAIAGAVACTSIAGANDPGGASAAFLAMTLALALCLLLGAWNGFLVSVLGIQP 138 Query: 118 FIVTLAGMFLARGLATTLSE-ESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVI 176 I TL M RG+A +++ + + +++ Y AV + LP ++ LI + FV+ Sbjct: 139 IIATLVLMTAGRGIAMLITDGQIVTVNNGTYAAVGAGFLVLP------VAILISLGVFVL 192 Query: 177 IAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSG 236 +AV+ T G + A+G N ++ L G+ ++Y ++ A +AG++ + + Sbjct: 193 VAVLTRKTALGMLIEAVGVNPTASRLAGVRSRTIVWTVYVFAALCAGVAGLMISANVSAA 252 Query: 237 YALGA-IGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTK 295 A A + +ELDAI AVVIGGT L+GG + GT++G +L+ + T + G + S T Sbjct: 253 DANNAGLWIELDAILAVVIGGTALSGGRYSLTGTLVGALLIQTLTTTVYTIG-IPSEVTL 311 Query: 296 IVIGLLLFFFILLQ 309 + L++ LLQ Sbjct: 312 VFKALVVIAVCLLQ 325 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: 344 Number of extensions: 21 Number of successful extensions: 4 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: 369 Length adjustment: 29 Effective length of query: 291 Effective length of database: 340 Effective search space: 98940 Effective search space used: 98940 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 24 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