Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_013402619.1 CALHY_RS03455 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >NCBI__GCF_000166355.1:WP_013402619.1 Length = 328 Score = 149 bits (377), Expect = 7e-41 Identities = 103/310 (33%), Positives = 166/310 (53%), Gaps = 12/310 (3%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L +F+ + F + + +++ + ALG+T VII+ GIDLS+G V+ LS V Sbjct: 24 LFLLFVFFSLASPNFCTFENIISIILATCVNGMLALGVTFVIITSGIDLSIGTVMTLSAV 83 Query: 76 VTSLLITEYQWHPLLAFVVILPLGT--LFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT 133 ++ + IT WH + V+ +GT L G + G +I KL PFI TL M +A+GLA Sbjct: 84 MSGVFIT--YWHLPVWLGVLGGIGTGMLCGFVNGIVISKMKLPPFIATLGMMMIAKGLAL 141 Query: 134 TLSEES--IAIDHPFYDAVAEMSIA---LPGNGALDLSSLIFILFFVIIAVVMHYTRFGT 188 +S + D P + +A SI +PG + + LIFILF +I +++ T G Sbjct: 142 VISGATPIYYTDAPSFSDIAMGSIIGKIIPG-ADIPNAILIFILFAIIANIILTKTAIGR 200 Query: 189 NVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDA 248 +AIG N+ +A L G+++ + I IY + F + GI+ S G ELDA Sbjct: 201 YDFAIGSNEEAARLSGLNVDRWKIIIYMLCGFFVGIGGILMASRLNSAQPALGQGYELDA 260 Query: 249 IAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308 IAAVVIGGT L+GG G ++GTV+G ++M + + S+ W ++ G+++ + L Sbjct: 261 IAAVVIGGTSLSGGEGSIIGTVIGALIMSTLTNGLRI-LSVPQEWQIVISGIIVIGAVYL 319 Query: 309 QKLLNGRKTQ 318 ++ R+T+ Sbjct: 320 D-IIRRRRTK 328 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: 352 Number of extensions: 23 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: 328 Length adjustment: 28 Effective length of query: 292 Effective length of database: 300 Effective search space: 87600 Effective search space used: 87600 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 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