Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012275184.1 SHAL_RS00270 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000019185.1:WP_012275184.1 Length = 307 Score = 96.7 bits (239), Expect = 6e-25 Identities = 84/268 (31%), Positives = 120/268 (44%), Gaps = 37/268 (13%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 +T++K L FG L AI + FE ++G I +GPNG GKTT +TG PT G I Sbjct: 3 ETVIKTTQLCRDFGSLKAIQNLDFEVEKGQIYGFLGPNGCGKTTAIRMLTGLLLPTAGDI 62 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKLMKASGY 130 + L +LP ++ Q L+ LTV ENL +A+ Sbjct: 63 --------EILGLQLPRDAEKLRLKIGYMTQKFSLYDDLTVKENLKFIAK---------- 104 Query: 131 TILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190 I GL + + A EL L L +AD AG + G ++RL +A A P Sbjct: 105 -IYGL----SRREQTARIQEL----LNTYGLEQKADQLAGSMSGGQKQRLGLAAATMHKP 155 Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250 ELL LDEP + ++P L + E GT+IL+ H M E + +LE G K Sbjct: 156 ELLFLDEPTSAVDPENRRDFWEKLFDL-CEQGTTILVSTHYMDEA-ERCHKLAILEAGVK 213 Query: 251 ISDGTPDHVKNDPRVIAAYLGVEDEEVE 278 DG+P+ + + +G + EVE Sbjct: 214 RVDGSPEQLMQN-------MGAQVVEVE 234 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: 165 Number of extensions: 11 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: 292 Length of database: 307 Length adjustment: 27 Effective length of query: 265 Effective length of database: 280 Effective search space: 74200 Effective search space used: 74200 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: 48 (23.1 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