Align ABC transporter permease (characterized, see rationale)
to candidate WP_004109052.1 RHSP_RS03470 sugar ABC transporter permease
Query= uniprot:A0A165KPZ4 (293 letters) >NCBI__GCF_000359745.1:WP_004109052.1 Length = 301 Score = 260 bits (664), Expect = 3e-74 Identities = 128/274 (46%), Positives = 178/274 (64%) Query: 12 KLVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVALKNL 71 K+ P + G +W V S T S++LP + GL QY RLW RW V+++NL Sbjct: 20 KIASIPMILTAVVIFLGGTIWTVVYSFTNSKLLPRLSFVGLDQYYRLWAAPRWTVSIENL 79 Query: 72 GIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGLG 131 ++G+ + SL+IG VLA L+DQKIR E RTI+LYP ALSF+VTG W+WLLNP G Sbjct: 80 AVYGILSMIFSLVIGFVLAALMDQKIRFENTFRTIFLYPFALSFIVTGLVWQWLLNPEFG 139 Query: 132 IEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAAQ 191 I+ +VR G+ F F L + IY V+IA +WQ G M L LAGLRGID+ I KAA+ Sbjct: 140 IQSVVRSLGWTTFTFDPLYTPSIVIYGVLIAALWQGTGLVMCLMLAGLRGIDEDIWKAAR 199 Query: 192 VDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPATFMY 251 VDG + + Y +V+P +RPVF +TL++++ +K +DLV+A T+GGPG A++VPA ++Y Sbjct: 200 VDGIPMWKTYLFVVIPMMRPVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPAKYVY 259 Query: 252 TMSFSRGQIGLGAASATMMLATVAALVIPYLYSE 285 F +G G A++TMML TVA ++IP+ Y E Sbjct: 260 DYMFQAQNLGQGFAASTMMLLTVAIVIIPWAYLE 293 Lambda K H 0.327 0.141 0.451 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: 337 Number of extensions: 14 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: 293 Length of database: 301 Length adjustment: 26 Effective length of query: 267 Effective length of database: 275 Effective search space: 73425 Effective search space used: 73425 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 (21.7 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