Align RhaQ (characterized, see rationale)
to candidate WP_068169524.1 HTA01S_RS08960 ABC transporter permease
Query= uniprot:Q7BSH2 (337 letters) >NCBI__GCF_001592305.1:WP_068169524.1 Length = 327 Score = 173 bits (438), Expect = 6e-48 Identities = 108/308 (35%), Positives = 163/308 (52%), Gaps = 17/308 (5%) Query: 38 LIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAIIALASTAM 97 LI +F S S F N T A + ++I+G IDLSV AI+ALA Sbjct: 21 LIVIF-SFTSDAFFTVGNGMTVALQVTSIAFLGIGATCVIITGGIDLSVGAILALAGVVA 79 Query: 98 GAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVLGD 157 AV+ G+ P +L G+ G CG+ NG+ V+VLKLP + T+G M + RG++ + Sbjct: 80 ALAVKAGVPVPLAMLAGLLVGALCGLINGLCVTVLKLPPFIATLGMMLVARGVALQITDA 139 Query: 158 QAYGKYPADFAYFGQGY--------------VVWV-FSFEFVLFIVLAVLFAILLHATNF 202 +A G FA G G VV+V + +L +VLAV +ILL+ Sbjct: 140 KAIGGLGESFAELGNGSLWRVVNIGPDGFPDVVFVGIPYPVLLMVVLAVAVSILLNRATL 199 Query: 203 GRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWEL 262 GR +YA+G+N AAR SG+ V+RV ++L+G+++G+ L SRL + +PS +EL Sbjct: 200 GRHLYAVGSNMEAARLSGVNVQRVTLFAYVLSGLLAGLTGCVLMSRLVTAQPSEGLMYEL 259 Query: 263 EVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTI 322 + + V+GG S+ GG G VI AFV+G++ GL + + I IGL+I++T+ Sbjct: 260 DAIAAAVIGGTSLTGGVGTISGT-VIGAFVIGILRNGLNMAGVSAFTQQILIGLVILLTV 318 Query: 323 AIPIIARR 330 I + R Sbjct: 319 WIDQMRHR 326 Lambda K H 0.330 0.145 0.423 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: 321 Number of extensions: 15 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: 337 Length of database: 327 Length adjustment: 28 Effective length of query: 309 Effective length of database: 299 Effective search space: 92391 Effective search space used: 92391 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