Alignments for a candidate for drdehyd-beta in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Sphingomonas histidinilytica UM2

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_079649976.1 B5X82_RS20220 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= metacyc::MONOMER-20833
         (739 letters)



>NCBI__GCF_900167915.1:WP_079649976.1
          Length = 740

 Score =  331 bits (848), Expect = 9e-95
 Identities = 246/767 (32%), Positives = 370/767 (48%), Gaps = 74/767 (9%)

Query: 7   LLDAPVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATS---AERGTQVPAFLEIRPDG 63
           ++D      RR FL    +GA V G GL LG  R   A +   AE   ++  ++ I PDG
Sbjct: 1   MIDMLEQADRRAFLK---IGAAV-GGGLMLGLMRPSVAVAGATAETAAELNGYVRIAPDG 56

Query: 64  TVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMS 123
              +++   E GQG  T +  ++ EELD       +E A           G +I GGS +
Sbjct: 57  IATIMAKNPEIGQGIKTMLPMLIAEELDIAWKDVRIEQADAD----ARRFGQQIAGGSYA 112

Query: 124 VRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSAL 183
             + +  +RR+GA AR ML+ A A++W     E  T+PG VVHAASGR LGYG LA  A 
Sbjct: 113 TPLHWDPLRRVGAAARQMLIAAAAQRWQCHPAECATEPGMVVHAASGRKLGYGALAGIAA 172

Query: 184 DMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRL 243
            MPVPD  ++ L+  + +R IGKP  ++D     TGK  + ID++V  M +A     P  
Sbjct: 173 TMPVPDLNNVPLKPEAGYRIIGKPTPQVDIDAIVTGKMQFGIDVEVPGMAYAVFAKCPVP 232

Query: 244 GMTVGSLRNQSQVEGMKGVHSVHVLPGA-----------VAVVAERWWHAKRAVEAIQVD 292
           G       N  ++   KGV +  V+ G+           VA+VA+ WW A++A + ++V+
Sbjct: 233 G-GKPVRANLDEISREKGVIATFVVDGSTDAPAGGLVSGVAIVADSWWRAEKARDKLRVE 291

Query: 293 WQEAAADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQ 352
           W   A  +      A F+++  R F    Q  T     +G+VA AL GA   VEA Y   
Sbjct: 292 WDGGAIAAH---SSAHFAAEAARLF---GQPATAVIRKDGEVAKALAGAARTVEADYFYP 345

Query: 353 YLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFF 412
           ++ HA LEP +  A    D  +EIW P QAP    A IA+  G+  A +T+H    GG F
Sbjct: 346 FIGHATLEPQNCTASVIGD-KVEIWAPTQAPARGIALIAETLGIPEANVTVHLIRCGGGF 404

Query: 413 GRHFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPV 472
           GR  +   A+P  +A  +AK  SRP+KL+WSR+++   D  RP    + +  LD  G  V
Sbjct: 405 GRRLI---ADPMVEAAYIAKKASRPVKLLWSRKDDMQHDFYRPAGFHRLKGGLDASGRLV 461

Query: 473 AIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSV 532
           A+     T G      GK     D +A E     +  +P+       ++     G  R+ 
Sbjct: 462 ALHDHFVTFGKD----GKVARSADLSASE---FPAQLVPHCLYESSLIECGIPTGPLRAP 514

Query: 533 GNSLNDFFYESFLDELADKGGHDPYELRLHLLR---------------------DNPRLT 571
           G++   F ++SF+DELA   G DPY+ +L +L                      D  R+ 
Sbjct: 515 GSNAIAFVFQSFMDELAHAAGKDPYQFQLDMLSEPRLLPTGRSLRPGSAEKVSFDTRRMA 574

Query: 572 TLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSI----ENGKVKVH 627
            +L+ A  +SG  KR          +  G+ +A  F SH    AEV++    ++G   V 
Sbjct: 575 DVLRKAASMSGWGKR-------RLPKRTGMGIACYF-SHLGYFAEVALVAVSKDGTPSVE 626

Query: 628 DIWQAIDPG-SIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQ 686
            +W A D G  I+NP++   QV G+V  G+   L ++     G     N++ + ++   +
Sbjct: 627 QVWVAADVGRHIINPSMAVNQVQGSVIDGIGSALFQQITIEKGGVVQANFNDHDLIRIDR 686

Query: 687 MARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
              V V  +++     G+GEP LP   PA+ NA+   TG+R+RSLP+
Sbjct: 687 APIVEVEFLKTDFPPTGLGEPALPPAIPAICNAIHAATGKRIRSLPI 733


Lambda     K      H
   0.317    0.134    0.394 

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: 1361
Number of extensions: 76
Number of successful extensions: 8
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: 739
Length of database: 740
Length adjustment: 40
Effective length of query: 699
Effective length of database: 700
Effective search space:   489300
Effective search space used:   489300
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: 55 (25.8 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:

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 2024 update 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