Align Probable glycine dehydrogenase (decarboxylating) subunit 1; EC 1.4.4.2; Glycine cleavage system P-protein subunit 1; Glycine decarboxylase subunit 1; Glycine dehydrogenase (aminomethyl-transferring) subunit 1 (uncharacterized)
to candidate WP_023431231.1 N177_RS05325 aminomethyl-transferring glycine dehydrogenase subunit GcvPA
Query= curated2:Q0BYP2 (447 letters) >NCBI__GCF_000496075.1:WP_023431231.1 Length = 447 Score = 533 bits (1374), Expect = e-156 Identities = 269/447 (60%), Positives = 327/447 (73%), Gaps = 1/447 (0%) Query: 1 MRYLPLTPEDRANMLATIGAKSVDDFYTDVPDAARLKGKIAGLPDHQGELAVERHLTKLA 60 MRYLPL+ +DRA ML IG S+DD + DVP AA L G + LP + E+ VER + A Sbjct: 1 MRYLPLSADDRAAMLHRIGVGSIDDLFADVPRAAWLDGPV-DLPAAKSEIEVERRFRRFA 59 Query: 61 AKNRSASSGPFFVGAGAYKHHVPATVDMIIQRSEFLTTYTPYQPEIAQGTLQTLFEFQTQ 120 +N +A FF GAGAY+HHVPATVD +IQRSEFLT+YTPYQPEI+QGTLQ LFEFQTQ Sbjct: 60 RRNLAAGDAAFFCGAGAYRHHVPATVDHLIQRSEFLTSYTPYQPEISQGTLQVLFEFQTQ 119 Query: 121 VASLTAMDVANASMYDGSTSCAEAAVMAARVTRRKKIILSGGLHPHYAAATRLLAEAQGL 180 V LT M+VANASMYDGST+ AEA +MA R+T+R + +++G LHPHYAA + Sbjct: 120 VCELTGMEVANASMYDGSTATAEAVLMAHRLTKRSRAVVAGNLHPHYAAVVETTSRLSSH 179 Query: 181 TVVQLPVAIDGEGELAKAVDGETACVIGQSPNVFGTVTDLSAVADAAHGKGALLVSVFTE 240 V L +G +L A+DG +CV+ Q+P+VFG DL +A+ AH GALLV+V TE Sbjct: 180 DTVFLTPTPEGGEDLLSAIDGTCSCVVVQTPDVFGHPVDLKPIAERAHEAGALLVAVVTE 239 Query: 241 AVSLGLVTPPGEMGADIAAGEGQSIGNGLNFGGPYVGLFSCREKLVRQMPGRLCGETVDA 300 AVSLGL+ PPG GADI EGQS+GNGLNFGGPYVGLF+ R+K +RQMPGR+CGETVD Sbjct: 240 AVSLGLMVPPGAQGADIVVAEGQSLGNGLNFGGPYVGLFATRQKFLRQMPGRVCGETVDV 299 Query: 301 DGKRGFVLTLSTREQHIRRDKATSNICTNSGLCALAFTSHMTLLGGKGLKQLAELNHEAA 360 +GKRG+VLTLSTREQHIRR+KATSNICTNSGLCALAFT H+TLLGG GL++LA LNH A Sbjct: 300 EGKRGYVLTLSTREQHIRREKATSNICTNSGLCALAFTVHLTLLGGVGLERLARLNHARA 359 Query: 361 IELADALGAVKGVEILTPRFFNEFAIRTPMDAEAVLAMLDEAGVVGGVRASRLFPGDHLG 420 LADAL V GVE+L FFNEF +R P A + L GV+GGV SRL PG+ L Sbjct: 360 TRLADALAEVPGVEVLNKAFFNEFTVRLPKPAAEIAEALAGKGVLGGVPMSRLRPGEGLD 419 Query: 421 DVILVAATECTTADDIAAYTDALKEII 447 D+++VAATE T +DI + LKE++ Sbjct: 420 DLLVVAATETNTDEDIDVFASCLKEVL 446 Lambda K H 0.318 0.134 0.382 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: 583 Number of extensions: 26 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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