GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Lutibaculum baratangense AMV1

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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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