Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_047213081.1 PATSB16_RS05695 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001931675.1:WP_047213081.1 Length = 284 Score = 233 bits (595), Expect = 3e-66 Identities = 126/271 (46%), Positives = 183/271 (67%), Gaps = 10/271 (3%) Query: 9 MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68 +S +TLL++E + + FGGL A++D SF +RG I LIGPNGAGKTTVFN ITG YKPT Sbjct: 10 VSGETLLELEGVGISFGGLRAVDDLSFRVQRGQIVGLIGPNGAGKTTVFNLITGVYKPTN 69 Query: 69 GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128 G I + Q + PD +I + + RTFQ IRLF+ +TVLEN++ +H ++ + Sbjct: 70 GHIRWR----GQEVTGLQPD-KIAAQG-IRRTFQTIRLFADMTVLENVVAGEHLQIKQRW 123 Query: 129 GYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188 GL+ +RE ++ A L++ +L+D A + A LPYG QRR+E+AR + Sbjct: 124 WQ---GLLNTPAQRREEQALVDRAMEVLQQLNLVDVAHENATSLPYGVQRRVELARTLVA 180 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 PEL+ LDEPAAGLN ESA LN +++IR + G +++L+EHDMSVVM ++D++VV+ +G Sbjct: 181 RPELIILDEPAAGLNEFESAGLNDTIRAIR-DAGVTVILVEHDMSVVMNVTDNIVVINFG 239 Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDEEVEE 279 +KI++G P ++N+P VI AYLG ED++ EE Sbjct: 240 KKIAEGKPAEIRNNPLVIEAYLGQEDDDEEE 270 Lambda K H 0.318 0.136 0.386 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: 229 Number of extensions: 11 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: 292 Length of database: 284 Length adjustment: 26 Effective length of query: 266 Effective length of database: 258 Effective search space: 68628 Effective search space used: 68628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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