GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glucosaminate-lyase in Desulfovibrio vulgaris Hildenborough

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 209218 AhpF family protein/thioredoxin reductase

Query= curated2:Q93HX6
         (320 letters)



>lcl|MicrobesOnline__882:209218 AhpF family protein/thioredoxin
           reductase
          Length = 579

 Score =  196 bits (498), Expect = 1e-54
 Identities = 127/308 (41%), Positives = 182/308 (59%), Gaps = 16/308 (5%)

Query: 2   VEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLT 61
           VEV  + +++LG+GPAG SAA+YA R+ L  +++     GGQ+T T  V+N+PG    + 
Sbjct: 268 VEVTETDLLVLGAGPAGLSAAIYAERSGLATVVLDKGIVGGQVTVTPVVENYPGFAD-IA 326

Query: 62  GPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLG 121
           G  L+E +  HA ++ T    + ++ +    +    T  +  +   A++ ATGA  R L 
Sbjct: 327 GIKLVEVLSSHARQYATIRENEGVDDIKLGRRIEVHTPRNV-FLARAVLFATGAQWRKLD 385

Query: 122 LPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETF 181
           +P E+ F GKGVS CA+CDGF YR + VAVVGGGNTA+ +AL+L N+   VT+IHRR+TF
Sbjct: 386 VPGEDRFYGKGVSYCASCDGFVYRGRKVAVVGGGNTALTDALHLRNLGVEVTVIHRRDTF 445

Query: 182 RAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELKVDGVFI 240
           RAEK L D L     EG I +  NA ++EV+GD   V G RL++   G   ++  DGVF+
Sbjct: 446 RAEKALQDSL---TREG-IPVIWNAVVEEVMGDT-EVRGVRLRDTKTGETRDVPFDGVFV 500

Query: 241 AIGHTPNTSLFE--GQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSA 298
           AIGH PN+      G     DG + V          T++  ++AAGDV   V RQ +T+ 
Sbjct: 501 AIGHVPNSEQAADLGVDLEPDGSIKVD-----RHMRTNIPRVYAAGDVIGGV-RQIVTAV 554

Query: 299 GAGCMAAL 306
           G+G  AAL
Sbjct: 555 GSGATAAL 562


Lambda     K      H
   0.318    0.135    0.386 

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: 445
Number of extensions: 23
Number of successful extensions: 4
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: 320
Length of database: 579
Length adjustment: 32
Effective length of query: 288
Effective length of database: 547
Effective search space:   157536
Effective search space used:   157536
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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