Alignments for a candidate for sdh in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Cereibacter sphaeroides ATCC 17029

Align D-sorbitol dehydrogenase large subunit (EC 1.1.99.21) (characterized)
to candidate WP_011842432.1 RSPH17029_RS17905 pyrroloquinoline quinone-dependent dehydrogenase

Query= metacyc::MONOMER-13708
         (740 letters)



>NCBI__GCF_000015985.1:WP_011842432.1
          Length = 724

 Score =  680 bits (1754), Expect = 0.0
 Identities = 356/726 (49%), Positives = 458/726 (63%), Gaps = 21/726 (2%)

Query: 19  PLIAHAQFAPAGAGGEPSSSVPGPGNASEPTENSPKSQSYFAGPSPYAPQAPGVNAANLP 78
           PL+A     P  A  EP+  +P    A +  E +P  Q     P+    QA    AA+  
Sbjct: 10  PLLALIAATPLAAQVEPAPGLPEADVAPQQAEPAPDLQPGDDAPTGQTEQAAPEGAAS-S 68

Query: 79  DIESIDPSQVPAMA----PQQSANPARGDWVAYGRDDHQTRYSPLSEITPENASKLKVAF 134
           +  S+  ++  A A    P Q       DW  +G D   TRYSPL EITPEN + L+ AF
Sbjct: 69  EGRSVAQAEAEAQAGVERPAQPQPEVGADWPFWGGDAQATRYSPLDEITPENVAGLERAF 128

Query: 135 VYHTGSYPRPGQVNKWAAETTPIKVGDGLYTCSAMNDIIKLDPATGKQIWRRNVDVKYHS 194
           VY TG  P      K++ ETTP+KVGD L  CSAMN +I +D  TG++ W  +  V   +
Sbjct: 129 VYRTGDMPSGDAEGKYSPETTPLKVGDDLLMCSAMNILISIDAETGEENWGYDPGVPAEA 188

Query: 195 IPYTAACKGVTYFTSSVVPEGQPCHNRLIEGTLDMRLIAVDAETGDFCPNFGHGGQVNLM 254
           IPY A+C+GV+ +T     EG  C  R+IEGTLD +L+AVDA TG  C  FG  G V+L 
Sbjct: 189 IPYGASCRGVSIYTDPAASEGALCATRVIEGTLDAKLVAVDASTGAPCEGFGENGTVDLW 248

Query: 255 QGLGESVPGFVSMTAPPPVINGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFVWAWDVN 314
           Q +GE VPG+ ++TAPP V+ G++V   +V DGQ   APSGVIRGYDA +G  VWAWD+ 
Sbjct: 249 QDIGERVPGWYAVTAPPAVVRGILVTGAQVKDGQAEDAPSGVIRGYDAVTGDLVWAWDLA 308

Query: 315 NSD-DHSQPTGNRHYSRGTPNSWATMTGDNEEGLVYVPTGNSAADYYSALRSDAENKVSS 373
             + + + P     Y+RGTPN W T   D E G VY+P GNS+ DYY + RS+AEN  ++
Sbjct: 309 APEANRAGPPEGEVYTRGTPNMWTTAVADEELGYVYLPMGNSSVDYYGSNRSEAENAYAT 368

Query: 374 AVVAIDVKTGSPRWVFQTAHKDVWDYDIGSQATLMDMPGPDGQTVPALIMPTKRGQTFVL 433
           ++VA+D  TG   W FQT   DVWDYD+GSQ TL+D  G      PA+++P+K+G  ++L
Sbjct: 369 SLVALDATTGEEVWHFQTVRHDVWDYDLGSQPTLLDWQG-----TPAILLPSKQGDLYIL 423

Query: 434 DRRTGKPILPVEERPAPSPGVIPGDPRSPTQPWSVGMPALRVPDLKETDMWGMSPIDQLF 493
           DR TG+P+ PVEE      G +  D  SPTQP S     LR+P L+  D WG + IDQL+
Sbjct: 424 DRATGEPLTPVEELTGLPQGDVEPDFISPTQPAS-AWATLRMPPLEPKDAWGFTAIDQLW 482

Query: 494 CRIKFRRANYVGEFTPPSVDKPWIEYPGYNGGSDWGSMSYDPQSGILIANWNITPMYDQL 553
           CRI+F RANY G FTPPS D+PWI+YPGYNGGSDWGS++ D Q G++IAN+N  P Y++L
Sbjct: 483 CRIQFHRANYEGYFTPPSSDRPWIQYPGYNGGSDWGSVAVDSQRGLIIANYNDVPNYNRL 542

Query: 554 VTRKKADSLGLMPIDDPNFKPGGGGAEGNGAMD---GTPYGIVVTPFW-DQYTGMMCNRP 609
           V R + +S   +PI +        G    GA D   G+PYGI V   W ++ TG+ C RP
Sbjct: 543 VPRDEVES---VPIHEQE-SGAQSGQNAEGAADPQAGSPYGISVNAGWRNEMTGIPCVRP 598

Query: 610 PYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTGGGLIFIG 669
           PYG I AID+  G+ V W  P GTAR NGP+G+P+ LP++IGTPNNGGSVVT GG+IFIG
Sbjct: 599 PYGHIRAIDLATGETV-WDRPFGTARRNGPFGIPSYLPFDIGTPNNGGSVVTAGGVIFIG 657

Query: 670 AATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQL 729
           AATDN  RAID  TG+ +W  VLP G QANP+TYE +G QYV I A GHHFM T V D +
Sbjct: 658 AATDNIFRAIDVETGETLWEDVLPAGAQANPITYEVDGRQYVMIAAVGHHFMETGVGDWM 717

Query: 730 VVYALP 735
           + YALP
Sbjct: 718 IAYALP 723


Lambda     K      H
   0.315    0.135    0.430 

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: 2082
Number of extensions: 172
Number of successful extensions: 10
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: 740
Length of database: 724
Length adjustment: 40
Effective length of query: 700
Effective length of database: 684
Effective search space:   478800
Effective search space used:   478800
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 (21.5 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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