GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Azospirillum brasilense Sp245

Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate AZOBR_RS07950 AZOBR_RS07950 hydroxypyruvate reductase

Query= reanno::psRCH2:GFF1145
         (423 letters)



>FitnessBrowser__azobra:AZOBR_RS07950
          Length = 420

 Score =  518 bits (1333), Expect = e-151
 Identities = 267/419 (63%), Positives = 329/419 (78%), Gaps = 2/419 (0%)

Query: 2   TLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGE 61
           T DP+ALL  +F +A+ +A P   +  HLPE   GR +V+GAGKAAA+MA+A+E  W+G 
Sbjct: 3   TTDPRALLTDMFRAAVASAQPALCVPPHLPEPPKGRTVVVGAGKAAASMAKAVEDHWKGP 62

Query: 62  LSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGG 121
           LSGLVVTRY H+  C+RIEVVEA+HPVPD+AG++ A+R+L++ ++L   D ++ L+SGGG
Sbjct: 63  LSGLVVTRYGHNVPCERIEVVEASHPVPDEAGQQAAKRILDIAASLGPDDLMLCLISGGG 122

Query: 122 SSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTY 181
           S+LLALPA GIS+ADKQA++KALLRSGA+I EMNCVRKHLSAIKGGRLA A   A V + 
Sbjct: 123 SALLALPAPGISMADKQAVSKALLRSGANITEMNCVRKHLSAIKGGRLA-AATKARVVSL 181

Query: 182 AISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDP 241
            ISDVPGD+ +VIASGPTV DPT+   AL +LE+Y I  P  V   L   R E+ KPGDP
Sbjct: 182 VISDVPGDDLSVIASGPTVPDPTSYADALAVLEKYGISPPQPVMDHLLAGRDESPKPGDP 241

Query: 242 MLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHG 300
            L R    L+ATPQ +L+ AAEVAR AG+TP+ILG+ LEGE+REVA VHAGIARQ+V H 
Sbjct: 242 RLERVSTILVATPQMALERAAEVARKAGVTPVILGNALEGESREVALVHAGIARQIVEHD 301

Query: 301 QPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSED 360
           QP A PCV+LSGGETTVTVRG GRGGRNAEFLLALT  L G+  V+ALA DTDGIDG+ED
Sbjct: 302 QPAAKPCVLLSGGETTVTVRGKGRGGRNAEFLLALTVALDGMKGVHALAADTDGIDGTED 361

Query: 361 NAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419
           NAGAL+ PD+ ARA   G+ A + LA+NDGY +F+AL DL+VTGPT TNVNDFRA+L++
Sbjct: 362 NAGALLSPDTLARAAEAGVNAKERLADNDGYSFFSALGDLLVTGPTLTNVNDFRAVLVV 420


Lambda     K      H
   0.316    0.134    0.384 

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: 523
Number of extensions: 24
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: 423
Length of database: 420
Length adjustment: 32
Effective length of query: 391
Effective length of database: 388
Effective search space:   151708
Effective search space used:   151708
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: 50 (23.9 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