Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate WP_011385258.1 AMB_RS14505 carbon monoxide dehydrogenase
Query= SwissProt::Q4J6M6 (281 letters) >NCBI__GCF_000009985.1:WP_011385258.1 Length = 261 Score = 124 bits (311), Expect = 2e-33 Identities = 94/281 (33%), Positives = 141/281 (50%), Gaps = 26/281 (9%) Query: 1 MYPPEFSYVRAESLQEALKFLEGNDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELN 60 M+P F Y+R +S+ EA+ +G + R LAGGQSL+ LKLR+ P ++DI RL EL Sbjct: 1 MFP--FDYLRPQSVAEAVCAHDGEER-RYLAGGQSLLAALKLRLAQPSALIDIARLPELA 57 Query: 61 YVKTSLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTIGDMQVRNMGTIGGAISNADP 120 + + +GA + + + +S +P + +IGD+QVRNMGT+GGA++NADP Sbjct: 58 GIHAEAGRLVVGAAVPHAQLAA----RSTIPALAQLAGSIGDLQVRNMGTLGGALANADP 113 Query: 121 ASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDTNKGELVTQIEVPVLDGYKTV 180 ASD + L A I + R + A DFF G F T GEL+ + P+ + Sbjct: 114 ASDHAAGVLGLGAEI----RTDRRVIAAADFFLGMFETALEPGELIVSVSYPL--PRRAS 167 Query: 181 YKKVVRRAGDYALASVALAIKLKGNEIED-IKLAYGGVHDKPFRAMEVEKNVIGKKLNDD 239 Y KV A Y + V +A E +D I++A G PFR E E + G D Sbjct: 168 YAKVRNPASGYPVVGVLVA------ETDDGIRVAVTGAASCPFRLTEFEMALAG-----D 216 Query: 240 LVKDIASKVSSQINPPS-DHRGSSWYRREVVKVLTMKAFKE 279 ++ ++ S D S+ YR ++ VL +A + Sbjct: 217 FSPAALEGLTVPVDDLSRDLHASAEYRAALIPVLARRALAQ 257 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: 173 Number of extensions: 10 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: 261 Length adjustment: 25 Effective length of query: 256 Effective length of database: 236 Effective search space: 60416 Effective search space used: 60416 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