Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896 Length = 281 Score = 122 bits (305), Expect = 1e-32 Identities = 83/272 (30%), Positives = 136/272 (50%), Gaps = 12/272 (4%) Query: 21 ANIILAILVVLTLGPIVFMVLTSLMDHNAIARGKWIA-PTRFSNYVEVFQKLPFGIYFRN 79 A ++LA V L P+V M+LTS I G ++ PT + G YF N Sbjct: 19 ATLLLAAAVYLI--PLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDVVGGYFWN 76 Query: 80 SLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKI 139 S+ + ++++ I + GY L+ ++F GS F L+L LP LLP K Sbjct: 77 SVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKF 136 Query: 140 KQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRV 199 L N+ GLV+V+ + + F+ R ++ SIP L +AAR+DG FT FL++ Sbjct: 137 G------LANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKI 190 Query: 200 MLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTA--RYDLLM 257 +LP+++P ++ I+ F W++ +F V+ I + + +T Y++ M Sbjct: 191 LLPMSIPIVMVCLIWQFTQIWNDFLFG-VVFASGDAQPITVALNNLVNTSTGAKEYNVDM 249 Query: 258 AAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 AA I +P L+++ K F+ G+T+GAVKG Sbjct: 250 AAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 Lambda K H 0.332 0.145 0.434 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: 264 Number of extensions: 15 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: 289 Length of database: 281 Length adjustment: 26 Effective length of query: 263 Effective length of database: 255 Effective search space: 67065 Effective search space used: 67065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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