Align DUF1338 domain-containing protein YdcJ (characterized)
to candidate BWI76_RS13295 BWI76_RS13295 DUF1338 domain-containing protein
Query= ecocyc::G6738-MONOMER (447 letters) >FitnessBrowser__Koxy:BWI76_RS13295 Length = 447 Score = 771 bits (1991), Expect = 0.0 Identities = 377/447 (84%), Positives = 409/447 (91%) Query: 1 MANSITADEIREQFSQAMSAMYQQEVPQYGTLLELVADVNLAVLENNPQLHEKMVNADEL 60 MAN+ITADEIRE FSQAMSAMYQQEVPQYGTLLELVADVNLA+LENNP LHE++ NADEL Sbjct: 1 MANTITADEIRESFSQAMSAMYQQEVPQYGTLLELVADVNLAILENNPTLHEQLANADEL 60 Query: 61 ARLNVERHGAIRVGTAQELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDASLA 120 ARLNVERHGAIRVGTA+ELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDA+LA Sbjct: 61 ARLNVERHGAIRVGTAEELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDAALA 120 Query: 121 RNPFRVFTSLLRLELIENEILRQKAAEILRQRDIFTPRCRQLLEEYEQQGGFNETQAQEF 180 RNPFRVFTSLLRLELI +E LR++AAEIL +RDIFT RCR+L+ +EQ+G F +A+EF Sbjct: 121 RNPFRVFTSLLRLELIADEALRKRAAEILARRDIFTSRCRELIALHEQKGEFTAAEAREF 180 Query: 181 VQEALETFRWHQSATVDEETYRALHNEHRLIADVVCFPGCHINHLTPRTLDIDRVQSMMP 240 VQ+ALETFRWH+ ATVDEETY ALH EHRLIADVVCFPGCHINHLTPRTLDIDRVQ++MP Sbjct: 181 VQQALETFRWHRHATVDEETYHALHEEHRLIADVVCFPGCHINHLTPRTLDIDRVQALMP 240 Query: 241 ECGIEPKILIEGPPRREVPILLRQTSFKALEETVLFAGQKQGTHTARFGEIEQRGVALTP 300 ECGI PK LIEGPPRR+VPILLRQTSFKALEE V+FAG+ +GTHTARFGEIEQRG+ALTP Sbjct: 241 ECGIAPKALIEGPPRRDVPILLRQTSFKALEEPVMFAGEHRGTHTARFGEIEQRGIALTP 300 Query: 301 KGRQLYDDLLRNAGTGQDNLTHQMHLQETFRTFPDSEFLMRQQGLAWFRYRLTPSGEAHR 360 KGR LYD LL AG G+DNL HQ HLQE F FPDSEFL+RQQGLA+FRYRLTP+GEAHR Sbjct: 301 KGRALYDRLLSEAGVGKDNLNHQRHLQEVFSPFPDSEFLLRQQGLAYFRYRLTPAGEAHR 360 Query: 361 QAIHPGDDPQPLIERGWVVAQPITYEDFLPVSAAGIFQSNLGNETQTRSHGNASREAFEQ 420 QA PGDDPQPLIERGWV+AQPI YEDFLPVSAAGIFQSNLGNE Q RSHGNASREAFE+ Sbjct: 361 QAFRPGDDPQPLIERGWVIAQPIIYEDFLPVSAAGIFQSNLGNEIQARSHGNASREAFEE 420 Query: 421 ALGCPVLDEFQLYQEAEERSKRRCGLL 447 ALGC V DEF LYQ+AEERSKRRCGLL Sbjct: 421 ALGCAVYDEFALYQQAEERSKRRCGLL 447 Lambda K H 0.320 0.135 0.397 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: 796 Number of extensions: 28 Number of successful extensions: 1 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: 447 Length of database: 447 Length adjustment: 33 Effective length of query: 414 Effective length of database: 414 Effective search space: 171396 Effective search space used: 171396 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 (21.8 bits) S2: 51 (24.3 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