Alignments for a candidate for sdh in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Rhodobacter johrii JA192

Align D-sorbitol dehydrogenase large subunit (EC 1.1.99.21) (characterized)
to candidate WP_069333494.1 C8J29_RS18500 PQQ-binding-like beta-propeller repeat protein

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



>NCBI__GCF_003046325.1:WP_069333494.1
          Length = 734

 Score =  688 bits (1775), Expect = 0.0
 Identities = 358/735 (48%), Positives = 465/735 (63%), Gaps = 29/735 (3%)

Query: 19  PLIAHAQFAPAGAGGEPSSSVPGPGNASEPTENSPKSQSYFAGPSPY------APQ---A 69
           PL+A     P  A  +P+  +P    A +  E SP +Q   AG +P       AP+   +
Sbjct: 10  PLLALIAATPLAAQVQPAQGLPEADVAPQQAEPSPDAQPGGAGDAPQGQTEQAAPEGAAS 69

Query: 70  PGVNAANLPDIESIDPSQVPAMA----PQQSANPARGDWVAYGRDDHQTRYSPLSEITPE 125
           P       P   S+  ++  A A    P Q       DW  +G D   TRYSPL EITPE
Sbjct: 70  PEAGTEAAPAGTSVAQAEAEAQALVERPAQPQPEVGADWPFWGGDAQATRYSPLDEITPE 129

Query: 126 NASKLKVAFVYHTGSYPRPGQVNKWAAETTPIKVGDGLYTCSAMNDIIKLDPATGKQIWR 185
           N + L+ AFVY TG  P      K++ ETTP+K+GD L  CSAMN +I +D ATG++ WR
Sbjct: 130 NVAGLERAFVYRTGDMPSAEADGKYSPETTPLKIGDDLLMCSAMNILISIDAATGEENWR 189

Query: 186 RNVDVKYHSIPYTAACKGVTYFTSSVVPEGQPCHNRLIEGTLDMRLIAVDAETGDFCPNF 245
            +  V   +IPY A+C+GV+ +T     EG  C  R+IEGTLD +L+AVDA TGD C  F
Sbjct: 190 YDPGVPAEAIPYGASCRGVSIYTDPAAAEGTLCATRVIEGTLDAKLVAVDAFTGDPCEGF 249

Query: 246 GHGGQVNLMQGLGESVPGFVSMTAPPPVINGVVVVNHEVLDGQRRWAPSGVIRGYDAESG 305
           G  G V+L Q +GE VPG+ S+TAPP V+ G++V   +V DGQ   APSGV+RGYDA +G
Sbjct: 250 GENGTVDLWQDIGERVPGWYSVTAPPAVVRGILVTGAQVKDGQAEDAPSGVVRGYDAVTG 309

Query: 306 KFVWAWDVNNSD-DHSQPTGNRHYSRGTPNSWATMTGDNEEGLVYVPTGNSAADYYSALR 364
             VWAWD+   + + + P     Y+RGTPN W T   D E G VY+P GNS+ DYY + R
Sbjct: 310 DLVWAWDLAAPEANRAGPPAGEVYTRGTPNMWTTAVADEELGYVYLPLGNSSVDYYGSNR 369

Query: 365 SDAENKVSSAVVAIDVKTGSPRWVFQTAHKDVWDYDIGSQATLMDMPGPDGQTVPALIMP 424
           S+AEN  ++++VA+D  TG   W FQT   DVWDYD+GSQ TL+D  G      PA+++P
Sbjct: 370 SEAENAFATSLVALDATTGEEVWHFQTVRHDVWDYDLGSQPTLLDWQG-----TPAILLP 424

Query: 425 TKRGQTFVLDRRTGKPILPVEERPAPSPGVIPGDPRSPTQPWSVGMPALRVPDLKETDMW 484
           +K+G  ++LDR TG+P+ P+EE      G +  D  SPTQP S     LR+P L+  D W
Sbjct: 425 SKQGDLYILDRATGEPLTPMEELTGLPQGDVEPDYISPTQPAS-AWATLRMPPLEPRDAW 483

Query: 485 GMSPIDQLFCRIKFRRANYVGEFTPPSVDKPWIEYPGYNGGSDWGSMSYDPQSGILIANW 544
           G + IDQL+CRI+F RANY G FTPPS D+PWI+YPGYNGGSDWGS++ D Q G++IAN+
Sbjct: 484 GFTAIDQLWCRIQFHRANYEGYFTPPSSDRPWIQYPGYNGGSDWGSVAVDSQRGLIIANY 543

Query: 545 NITPMYDQLVTRKKADSLGLMPIDDPNFKPGGGGAEGNGAMD---GTPYGIVVTPFW-DQ 600
           N  P Y++LV R + +S   +PI +        G    GA D   G+PYGI V   W ++
Sbjct: 544 NDVPNYNRLVPRDEVES---VPIHEQE-SGAQAGENAEGAADPQAGSPYGISVNAGWRNE 599

Query: 601 YTGMMCNRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVV 660
            TG+ C RPPYG I AID++ G+ V W  P GTAR NGP+G+P+ LP++IGTPNNGGSVV
Sbjct: 600 MTGIPCVRPPYGHIRAIDLETGETV-WDRPFGTARRNGPFGIPSYLPFDIGTPNNGGSVV 658

Query: 661 TGGGLIFIGAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHF 720
           T GG+IF+GAATDN  RAID  TG+ +W  VLP G QANP+TYE +G QYV I A GHHF
Sbjct: 659 TAGGVIFMGAATDNLFRAIDVETGETLWQDVLPAGAQANPITYEVDGRQYVMIAAVGHHF 718

Query: 721 MMTPVSDQLVVYALP 735
           M T V D ++ YALP
Sbjct: 719 METGVGDWMIAYALP 733


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: 2090
Number of extensions: 160
Number of successful extensions: 9
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: 734
Length adjustment: 40
Effective length of query: 700
Effective length of database: 694
Effective search space:   485800
Effective search space used:   485800
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 Sep 24 2021. 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 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