Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__PV4:5210167 Length = 265 Score = 194 bits (493), Expect = 2e-54 Identities = 105/252 (41%), Positives = 155/252 (61%), Gaps = 2/252 (0%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 + +L V IS FGG++AL+DV ++RG V+ +IGPNGAGKT+ N I+G Y P GT Sbjct: 3 DTILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTI 62 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGR-HIRTGSGLFGAVFRTK 125 + + A GI RTFQN+ LF M+ L+N+MVGR H+ + L G ++ Sbjct: 63 HFDNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMVGRHHLMKNNWLTGPLYWAS 122 Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185 + EE A ++ +E++D++ I A TLSYG ++R+E+ARA+A +P+LI LDEP Sbjct: 123 PAQKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDEPM 182 Query: 186 AGMNATEKVQL-RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 AGMN EK + R ++D T+++IEHD+ +VM + V VLD+GK++ G P V Sbjct: 183 AGMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPEAV 242 Query: 245 QKNEKVIEAYLG 256 +E V +AYLG Sbjct: 243 MADEHVRQAYLG 254 Lambda K H 0.319 0.137 0.384 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: 193 Number of extensions: 8 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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 (21.7 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