Align ABC transporter (characterized, see rationale)
to candidate Ac3H11_909 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_909 Length = 374 Score = 243 bits (620), Expect = 6e-69 Identities = 116/238 (48%), Positives = 173/238 (72%), Gaps = 4/238 (1%) Query: 2 IKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61 + +++ NV+KQ G + LRDVSL+I +GE + +GPSGCGK+TLLR+IAGL++ G + Sbjct: 1 MSIEIRNVSKQFGDFQALRDVSLDIQSGELIALLGPSGCGKTTLLRIIAGLETADVGTIH 60 Query: 62 IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLA----KTDKTSLRERVLKT 117 G D+ RER VG VFQ YAL+ HM+V++N++FGL++ + + ++++V+ Sbjct: 61 FSGEDTTDVHVRERNVGFVFQHYALFRHMTVFENVAFGLRVKPRSERPSEAQIKKKVMDL 120 Query: 118 AQILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIA 177 +++QLD L +R P +LSGGQRQR+A+ RA+A EP +LL DEP LDA +R ++R + Sbjct: 121 LKLVQLDWLAERYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLR 180 Query: 178 RLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLG 235 RLHD L T I+VTHDQ EA+ +AD++VV+N GR+EQ GSP++++++PAS FV GFLG Sbjct: 181 RLHDELHVTSIFVTHDQEEALEVADRVVVINQGRIEQSGSPQQVWDQPASPFVYGFLG 238 Lambda K H 0.320 0.137 0.394 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: 362 Number of extensions: 12 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: 381 Length of database: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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