Align Solute-binding protein Bpro_3107 (characterized)
to candidate Ac3H11_161 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_161 Length = 323 Score = 175 bits (444), Expect = 1e-48 Identities = 104/300 (34%), Positives = 165/300 (55%), Gaps = 4/300 (1%) Query: 16 LAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKVFNKQAL 75 L+ L + AAQ T S T A + A+ + +EK++ G++K++ F AL Sbjct: 10 LSLALGFVATAAAQTTMRISIST--AQNSHQGIAIDTFAKEVEKRTSGRYKVQTFYNGAL 67 Query: 76 GSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGPVGDEIL 135 G E+E+I+ V++G + + GP+ P T++ +PFLF AH R LDGP+G E+L Sbjct: 68 GGERESIEAVQLGTQELAFSSTGPIPNFVPETKILDVPFLFRDKAHARAVLDGPIGQEML 127 Query: 136 KSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVSAMGANATP 194 +S GF LA+ ++G R + +K+ + T D KGLK+R ++ + +A G TP Sbjct: 128 TKFDSKGFKALAWAENGFRHMTNSKRSVNTPEDLKGLKMRTMENPVHIAAYKGFGIITTP 187 Query: 195 MPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKIIYDKLP 254 M + EV+T L+ G +D EN +P +AK + K + T H +P I VM+K +DKL Sbjct: 188 MAFPEVFTALQQGTVDGQENPLPVIISAKFDQVQKHLTLTGHVYSPAIFVMNKGSFDKLS 247 Query: 255 KAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVE-VDKKSFQAVMGPVYDKF 313 A++ AAKE R + DE +AK +A+++A G +V+ DK F A + PV +F Sbjct: 248 AADKQAFIDAAKEGTKANRARVDEDDAKGVADLRAKGMTVVDNPDKSKFVAALAPVNAEF 307 Lambda K H 0.316 0.130 0.362 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: 245 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: 330 Length of database: 323 Length adjustment: 28 Effective length of query: 302 Effective length of database: 295 Effective search space: 89090 Effective search space used: 89090 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 (21.6 bits) S2: 48 (23.1 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