Alignments for a candidate for rhaB in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaB in Pseudarthrobacter sulfonivorans Ar51

Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate WP_058931374.1 AU252_RS14790 rhamnulokinase

Query= reanno::Koxy:BWI76_RS00680
         (488 letters)



>NCBI__GCF_001484605.1:WP_058931374.1
          Length = 497

 Score =  311 bits (798), Expect = 3e-89
 Identities = 193/478 (40%), Positives = 257/478 (53%), Gaps = 26/478 (5%)

Query: 8   AVDLGASSGRVMLASYQPGQQTLA-----LREIHRFTNSLQKVDGFDCWDLDSLEGEIRR 62
           AVD+GASSGRV+L   + G    A     L  +HRF N + ++ G   WD D+L  E+  
Sbjct: 21  AVDIGASSGRVILGRIKDGSSATADGSVELETVHRFPNGVVELPGGLRWDFDALFAEVLA 80

Query: 63  GLEKVCEQGILID----SIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQL 118
           GL        L D    SIGIDTW VDY L++  G+ +  P SYRD R++  +     +L
Sbjct: 81  GLTAAGTAAKLQDETITSIGIDTWAVDYGLVNAAGELMAQPFSYRDDRSRAAVAPVHRKL 140

Query: 119 GRAEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTN 178
             A +Y  +G+QFL FNTLYQL        E       ALLIPD  +F LTG    E TN
Sbjct: 141 DPARLYATTGLQFLQFNTLYQLAT------ERDLDGLQALLIPDLIAFLLTGQRRTESTN 194

Query: 179 ATTTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHI------PVVA 232
           A+TT L +  +  W  + L   G P++ F     PG  +G  +      +       VVA
Sbjct: 195 ASTTGLFDAVAGEWATEFLTALGLPKKLFPPLIEPGETVGTLLPEIATRVGLPTGTKVVA 254

Query: 233 VASHDTASAVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYR 292
           V SHDTASAV A P   ++ AY+SSGTWSL+G E   P  ++A+  AN TNE G +G  R
Sbjct: 255 VGSHDTASAVAAVPAQDEDFAYISSGTWSLVGLELNQPVLTEASRAANFTNERGVDGTIR 314

Query: 293 VLKNIMGLWLLQRVLR----EQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAE 348
            L+N+ GLWLL    R    E    +L  L+A  +ALP     I+ +D  FI PD+M   
Sbjct: 315 YLRNMGGLWLLSECQRTWGAEGFTPELADLLAAASALPPGGPQINPDDSAFIAPDNMPHR 374

Query: 349 IQAACRESGQPVPDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNEL 408
           I+A  R +G  +PD    + RCI DSLA  Y R + +   L  +    +HIVGGG QN L
Sbjct: 375 IRATVRHTGDLLPDDPVAITRCIMDSLATGYARAIADAERLADRTVDVVHIVGGGSQNRL 434

Query: 409 LNQLCADACGITVVAGPVEASTLGNIGIQLMTLDEL-NNVDEFRQVVRQNYALTTFTP 465
           L QL AD  G  VVAGPVEA+ +GN+ +Q      +   + E R++V  ++ L TFTP
Sbjct: 435 LCQLTADTTGKKVVAGPVEATAVGNVLVQARAAGHITGGLTELRRLVVSSHELQTFTP 492


Lambda     K      H
   0.320    0.135    0.413 

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: 552
Number of extensions: 27
Number of successful extensions: 6
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: 488
Length of database: 497
Length adjustment: 34
Effective length of query: 454
Effective length of database: 463
Effective search space:   210202
Effective search space used:   210202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources