GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpA in Sinorhizobium fredii NGR234

Align Anaerobic glycerol-3-phosphate dehydrogenase subunit A2; G-3-P dehydrogenase A2; G3PDH A2; EC 1.1.5.3 (characterized)
to candidate WP_012709582.1 NGR_RS26605 glycerol-3-phosphate dehydrogenase

Query= SwissProt::D4GQU6
         (563 letters)



>NCBI__GCF_000018545.1:WP_012709582.1
          Length = 505

 Score =  121 bits (304), Expect = 6e-32
 Identities = 141/461 (30%), Positives = 189/461 (40%), Gaps = 67/461 (14%)

Query: 3   YSVVVIGGGATGTGTARDLAMRGFDVTLVERGNLTEGTTGRTHGHLHSGARYAVSDKESA 62
           + V VIGGG  G G ARD   RG+ V L E  +   GT+  +   +H G RY    +   
Sbjct: 7   FDVFVIGGGINGCGIARDAVGRGYSVALAEMDDFASGTSSGSTKLIHGGLRYLEHYEFRL 66

Query: 63  V-DCMRENRVLHRIAGHCIEDTGGLFVQLEGDS-------------DDYFERKLAGCAEC 108
           V + + E  VL  +A H I     +    +G               D    RKL      
Sbjct: 67  VREALMEREVLWAMAPHVIWPMRFVLPYHKGGPRPAWLIRLGLFLYDHIGGRKLLPATST 126

Query: 109 DIPTEVISGEEARRREPYLTDAVERAIWVPDGAVDPFRLCVANAASAVEHGARIETHAEV 168
              T   +G   +R     T A E +    DG VD  RL V NA  A + GARI     V
Sbjct: 127 LDMTRDAAGGPLKR---LFTKAFEYS----DGWVDDARLVVLNARDAADRGARIMARTRV 179

Query: 169 VDLVVEGGRVAGVEVKRQGPNHHSEGAAGDTETFEADYVVSATGAWAGQLAAMAGVDLEM 228
           V    E GR A +E +        +   G  ET  A  +V+ATG W         VD  +
Sbjct: 180 VSARRENGRWA-IETE--------DAQTGARETLRARLLVNATGPW---------VDRVL 221

Query: 229 AISKGAMVVTNVRQLD---TVINRCL----------PKGEGDTIIPHETT-VLLGAND-D 273
           A + G   V NVR +     V+ R            P G     IP++    L+G  D D
Sbjct: 222 ADTLGKNDVHNVRLVQGSHIVVKRKFDDPRAYFFQNPDGRIMFAIPYQNDFTLIGTTDRD 281

Query: 274 PVDDPDDYPEEQWEVDMMIDIASEMV--PVVADARMIRAYWGVRPLYDPNPKSTTDPGDV 331
              +P D      E+D +   ASE    PV  D  ++  Y  VRPLYD       +    
Sbjct: 282 FTGNPADVRISDAEIDYLCKSASEYFSDPVTTDD-IVWTYSAVRPLYDDGASKAQE---A 337

Query: 332 TRNYFVLDHAERDGVAGFASVVGGKLTTYREMAESVSDHVCEVLGVEEPCRTDEVPLP-G 390
           TR+Y VL    ++G A   +V GGKLTTYR +AES  + + E +G +    T    LP G
Sbjct: 338 TRDY-VLRVEGQNGQAPLLNVFGGKLTTYRRLAESALEKIGEAIGTKGSKWTATSHLPGG 396

Query: 391 SADPSALDEYMDEFDLRSPI-----ARRSGQRLGDRAPEVL 426
               +A D  +D    R P      ARR  +  G +A  +L
Sbjct: 397 DFAATAYDTEVDMLKARYPFLALSHARRLVRLYGTQAASLL 437


Lambda     K      H
   0.316    0.134    0.405 

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: 662
Number of extensions: 30
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 563
Length of database: 505
Length adjustment: 35
Effective length of query: 528
Effective length of database: 470
Effective search space:   248160
Effective search space used:   248160
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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