Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011385951.1 AMB_RS18185 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000009985.1:WP_011385951.1 Length = 274 Score = 221 bits (562), Expect = 2e-62 Identities = 118/243 (48%), Positives = 171/243 (70%), Gaps = 9/243 (3%) Query: 7 KVLLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDG- 64 ++LL V ++V Y + V +GV +V +G++V+L+G NGAGK+TT+KAI+G L DG Sbjct: 12 EILLSVNNIEVVYDDVILVLRGVSLDVPKGKIVTLLGPNGAGKSTTLKAISGLLGTEDGE 71 Query: 65 ----NIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDK-AGIL 119 NI ++G+ I + D+V+ G+ V EGR + MT+ ENL++GA+ RKD A + Sbjct: 72 VTRGNITFMGEEIANRAPEDIVRRGIFQVMEGRRIIEDMTVIENLRLGAFTRKDGGAAVR 131 Query: 120 ADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVD 179 DIEK+F FPRL+ER LAG +SGGEQQMLA+GRA+M++PK++LLDEPSMGLSP++V Sbjct: 132 DDIEKVFHYFPRLKERTG-LAGYLSGGEQQMLAIGRAMMARPKMILLDEPSMGLSPLLVK 190 Query: 180 KIFEVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAA 238 ++F ++ + A G+T++LVEQNA AL IA GY+MESG I + G + L+N+ V+ Sbjct: 191 EVFAIIETLCAETGITMLLVEQNARMALKIAQFGYIMESGKIVLDGAKEDLVNNEDVKEF 250 Query: 239 YLG 241 YLG Sbjct: 251 YLG 253 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: 203 Number of extensions: 13 Number of successful extensions: 5 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: 274 Length adjustment: 24 Effective length of query: 218 Effective length of database: 250 Effective search space: 54500 Effective search space used: 54500 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 17 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