GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Acidovorax sp. GW101-3H11

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Ac3H11_2341 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2341
          Length = 322

 Score =  213 bits (542), Expect = 5e-60
 Identities = 125/281 (44%), Positives = 166/281 (59%), Gaps = 11/281 (3%)

Query: 32  KAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGI 91
           +A P+G L  +  E   +VT  +  +  E++   P L++I+ + VG+D +DI  AT RG+
Sbjct: 36  QADPQGFLAAQGAEFSGVVTTASIGLQGEVIAALPHLQVISSFGVGFDALDIGTATARGV 95

Query: 92  YVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGK 151
            V  TPGVL D  AD+AFAL+L V+R I  +D FVR G+W K+         LG  + GK
Sbjct: 96  QVGYTPGVLNDCVADMAFALMLDVSRGIAASDRFVRQGQWPKARFA------LGTRVSGK 149

Query: 152 TLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKE-SDFISL 210
            LGIVG GRIGQA+A+RA GF M++ Y++R       E     Y +  T L + +D++ L
Sbjct: 150 RLGIVGMGRIGQAVAERAAGFRMEVSYHNR----RPAEGCALSYFESLTALAQWADYLVL 205

Query: 211 HVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEE 270
            V     T H++    L  + P   LIN +RG+VVD  ALI AL E  IAGAGLDVF+ E
Sbjct: 206 TVAGGAGTRHLVNRDVLDALGPQGYLINVARGSVVDEAALIDALAERRIAGAGLDVFDNE 265

Query: 271 PYYNEELFKLKNVVLAPHIGSATHEAREGMAELVAKNLIAF 311
           P     L  L NVVL PH  SATHE R  MA+LV +NL AF
Sbjct: 266 PQVPAALMALDNVVLTPHTASATHETRRAMADLVLENLHAF 306


Lambda     K      H
   0.317    0.137    0.392 

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: 235
Number of extensions: 12
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: 331
Length of database: 322
Length adjustment: 28
Effective length of query: 303
Effective length of database: 294
Effective search space:    89082
Effective search space used:    89082
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. 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