Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_4987 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4987 Length = 272 Score = 213 bits (541), Expect = 4e-60 Identities = 113/248 (45%), Positives = 168/248 (67%), Gaps = 7/248 (2%) Query: 1 MAEKSNKVLLQVKGLKVAYGGI-QAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL 59 M + + +L+V ++V Y + QA++G+ V G++V+L+GSNGAGK+TT+KAI+G L Sbjct: 1 MTQPTPAHVLEVNNIEVIYNKVVQALRGLSLAVPRGQIVALLGSNGAGKSTTLKAISGLL 60 Query: 60 SMNDGNIE-----YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKD 114 ++ DG +E + G+ LV+ GL V EGR VF +T+ ENL Y Sbjct: 61 ALEDGVVESGSIHFNGQPTAAVAPQQLVRNGLSHVMEGRRVFEDLTVEENLVAATYALTG 120 Query: 115 KAGILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLS 174 ++G D + +++ FPRL ER+ LAG +SGGEQQMLA+GRAL++QP+++LLDEPS+GLS Sbjct: 121 RSGTTPDFDLVYSYFPRLHERRKGLAGYLSGGEQQMLAIGRALIAQPQLILLDEPSLGLS 180 Query: 175 PIMVDKIFEVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDP 233 P +V+ IF ++ + A G +++LVEQNA+ ALA+A RGY+ME+G I + G ++L NDP Sbjct: 181 PKLVEDIFTIIARINAERGTSMLLVEQNATVALAVAHRGYIMENGKIVIDGTAERLANDP 240 Query: 234 KVRAAYLG 241 VR YLG Sbjct: 241 DVREFYLG 248 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: 201 Number of extensions: 12 Number of successful extensions: 3 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: 272 Length adjustment: 24 Effective length of query: 218 Effective length of database: 248 Effective search space: 54064 Effective search space used: 54064 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