GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Algiphilus aromaticivorans DG1253

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate WP_084191695.1 U743_RS04135 FAD-dependent oxidoreductase

Query= curated2:O86567
         (372 letters)



>NCBI__GCF_000733765.1:WP_084191695.1
          Length = 947

 Score =  173 bits (439), Expect = 2e-47
 Identities = 136/379 (35%), Positives = 176/379 (46%), Gaps = 27/379 (7%)

Query: 7   RRTALDATHRALGATMTDFAGWDMPLRYGSERE-------EHVAVRTRAGLFDLSHMGEI 59
           R T L   H+ALGA   +   W  P  YG   E       E  AVR+RAGL D+S +G+I
Sbjct: 565 RLTPLHEAHQALGAHFMEAGEWLRPAFYGDAAEADSAIAAEVAAVRSRAGLIDVSTLGKI 624

Query: 60  TVTGPQAAELLNFALVGNIGTVKPGRARYTMICREDGGILDDLIVYRLEEAEYMVVANAS 119
            V G  A  LL  A    +  +  GR RY ++    G I+DD IV RL E  Y V   + 
Sbjct: 625 EVLGADAGRLLEAAYTMRMTNIAVGRTRYALMVDSSGVIVDDGIVGRLAEDRYYVTTTSG 684

Query: 120 NAQVVLDALTERAA--GFDAEVRDDRDAYALLAVQGPESPGILASLTD---ADLDGLKYY 174
           +A      L+  A   G D  + +       L + GPE+  +LA L      D D   Y 
Sbjct: 685 HAAATFRTLSRCALEWGLDVHLLNRTGQLGALNLAGPEARRLLAPLVSDVGLDEDAFPYL 744

Query: 175 AGLPGTVAGVPALIARTGYTGEDGFELFVKPEHAVGLWQALTGAGEAAGLIPCGLSCRDT 234
               G V G PA +AR G+ GE G+EL +       +WQAL    +A    P G+  +  
Sbjct: 745 GIREGRVCGHPARLARVGFVGELGYELHLDARATAEVWQALMRDADAPR--PFGVEAQRL 802

Query: 235 LRLEAGMPLYGNELSTALTPFDAGLGRVVKFEKEGDFVGRAALTEAAERAASRPPRVLVG 294
           LRLE G  + G +      PF+AG+G  V F+K   F GRAAL +   R   R    LVG
Sbjct: 803 LRLEKGHIIVGQDTDGLSDPFEAGMGWAVHFKKP-FFNGRAALQQLKPRMRRR----LVG 857

Query: 295 --LVAEGRRVPRSGYRVVAGGEVIGEVTSGAPSPTLGRPIAMAYVDPAHAAPGTEGVGVD 352
             L A    +PR  + V+  G + G VTS A SPTL  P+ +A VD   AA    G  + 
Sbjct: 858 FALPAGVETLPRECHLVIRDGVIAGRVTSIAHSPTLRHPVGLAMVD---AALADSGEALQ 914

Query: 353 IRGSH---EPYEVVALPFY 368
           IRG        E  A PFY
Sbjct: 915 IRGDDGRMHRAEQRATPFY 933


Lambda     K      H
   0.318    0.137    0.400 

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: 921
Number of extensions: 55
Number of successful extensions: 5
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: 372
Length of database: 947
Length adjustment: 37
Effective length of query: 335
Effective length of database: 910
Effective search space:   304850
Effective search space used:   304850
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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