Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028320689.1 H567_RS0105885 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000422285.1:WP_028320689.1 Length = 263 Score = 191 bits (486), Expect = 9e-54 Identities = 103/240 (42%), Positives = 162/240 (67%), Gaps = 8/240 (3%) Query: 9 LLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN-- 65 +L++K ++V Y + V KGV EV + +V+L+G+NGAGK+TT+KA++G L + DG Sbjct: 1 MLKIKNIEVKYHEVILVLKGVSIEVPKAGIVALLGANGAGKSTTLKAVSGLLKVEDGEVT 60 Query: 66 ---IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADI 122 IE+ G+ I + A + K G+V V EGR VF +T+ ENL++GA++RK + + Sbjct: 61 DGGIEFEGQMIHHEPAAKIAKMGIVQVIEGRKVFEHLTVEENLKVGAHLRKT-GSVKDKL 119 Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIF 182 E ++ FPRLR+++ + AG +SGGEQQM +GRALM++PK++LLDEPSMGL+P+++ +IF Sbjct: 120 ELVYHYFPRLRQKRSETAGFVSGGEQQMTVVGRALMTEPKLVLLDEPSMGLAPMLIHEIF 179 Query: 183 EVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 ++ + ++I+LVEQNA AL +A YVME+G I M ++L + ++ YLG Sbjct: 180 NIITQLNKEEKISILLVEQNAKLALNVAPYAYVMETGRIVMDDTAEKLSQNEDIKDFYLG 239 Lambda K H 0.317 0.136 0.373 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: 195 Number of extensions: 7 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: 242 Length of database: 263 Length adjustment: 24 Effective length of query: 218 Effective length of database: 239 Effective search space: 52102 Effective search space used: 52102 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: 46 (22.3 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