Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate SMc03103 SMc03103 carbon monoxide dehydrogenase medium subunit transmembrane protein
Query= SwissProt::Q4J6M6 (281 letters) >FitnessBrowser__Smeli:SMc03103 Length = 265 Score = 123 bits (309), Expect = 4e-33 Identities = 88/275 (32%), Positives = 140/275 (50%), Gaps = 19/275 (6%) Query: 5 EFSYVRAESLQEALKFLEGNDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELNYVKT 64 E +Y RA S++EA + + L+GG +LIP +K R+ +P ++D+ + E+ + Sbjct: 3 ETNYHRASSVEEAANLMGTAAEGKYLSGGMTLIPTMKQRLAAPSDLVDLRHIAEMKGITV 62 Query: 65 SLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTIGDMQVRNMGTIGGAISNADPASDM 124 V IGA T + ++ ++ + + P + IGD VR+MGTIGG+I+N DPA+D Sbjct: 63 DGRSVRIGAATTHEEVATSAALAAACPAICGLASHIGDPHVRHMGTIGGSIANNDPAADY 122 Query: 125 PVVLTALNATIILSSASGSRSVKALDFFKGPFTTDTNKGELVTQI--EVPVLDGYKTVYK 182 P + AL+A I+ + R VKA DFF G F T GE+VT + E P K Y+ Sbjct: 123 PAAMLALDAVIV----TDRREVKAEDFFTGLFETALEDGEIVTAVRFEAPA----KAAYQ 174 Query: 183 KVVRRAGDYALASVALAIKLKGNEIEDIKLAYGGV-HDKPFRAMEVEKNVIGKKLNDDLV 241 K A YA+ V + + G +++A G D FR ++E + + V Sbjct: 175 KFPNPASRYAMTGVFVVRRDDGG----VRVAVTGAGSDGVFRHRDLEA-ALAANWSPGAV 229 Query: 242 KDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKA 276 ++ S + SD S+ YR +VKV+T +A Sbjct: 230 ANVQVDDSDLL---SDIHASAAYRANLVKVMTKRA 261 Lambda K H 0.316 0.134 0.372 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: 147 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: 281 Length of database: 265 Length adjustment: 25 Effective length of query: 256 Effective length of database: 240 Effective search space: 61440 Effective search space used: 61440 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: 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