Alignments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

Align D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS22805 HSERO_RS22805 GMC family oxidoreductase

Query= metacyc::MONOMER-12745
         (594 letters)



>FitnessBrowser__HerbieS:HSERO_RS22805
          Length = 590

 Score =  573 bits (1478), Expect = e-168
 Identities = 286/589 (48%), Positives = 392/589 (66%), Gaps = 9/589 (1%)

Query: 8   VDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYP-DGNYPQVIDELTYSVRKKLF 66
           VD VIVG GW G++MA EL +AGL V ALERGP  D  P D  YP+  D+  Y+ R K+F
Sbjct: 9   VDVVIVGLGWAGSLMAIELAQAGLKVRALERGP--DRPPEDFAYPKPADQYGYATRNKVF 66

Query: 67  QDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRMRSHYEE 126
                  +T+R++    ALP R+ GAF PG GVGG+GLHW+ V  R  P +L+++++ ++
Sbjct: 67  ATPRDAALTVRYNTAQQALPTRKWGAFAPGTGVGGSGLHWTAVLIRATPTDLKLKTYADQ 126

Query: 127 RYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVRGQLVGDGKGGNPYAPD 186
            Y  + +  +M I+DF  ++ E+EP +D+ +KV G SG    +RGQ+     GG+P+   
Sbjct: 127 AYKHSNLDPEMRIKDFPFTWNEIEPHYDFFDKVCGLSGTTGNLRGQIQ---PGGDPFEGP 183

Query: 187 RSDHFPLESQKNTYSAQLFQKAANDVGYKPYNLPSANTSGPYTNPYGAQMGPCNFCGFCS 246
           RS+ +PL +  +TY+  LF   A  +GY P+  PSAN S  +TNPYGAQ+ PCN+CGFCS
Sbjct: 184 RSNPYPLPALHDTYNNTLFADVARKLGYHPFPNPSANVSQAWTNPYGAQIAPCNYCGFCS 243

Query: 247 GYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDGQGREIE 306
            Y C  YSKASP   IL  +K LPNF+ + N++V+RV+L + K  A GVTYVD   +E+ 
Sbjct: 244 KYPCLNYSKASPQTTILDVVKRLPNFDYKVNANVIRVDLHADKKTARGVTYVDENMKEVF 303

Query: 307 QPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFDKDVHTN 366
           QPA +VIL +FQF NVRLMLLSGIGKPYDPIT  GV+G+N+A+ +      +F KD H N
Sbjct: 304 QPAKIVILSSFQFANVRLMLLSGIGKPYDPITETGVIGRNYAFLSNGGATLFF-KDKHFN 362

Query: 367 NFIGAGGNGVAVDDFNADNFDHGPH-GFVGGSPMWVNQAGSRPIAGTSNPPGTPAWGSAW 425
           +F  AG  G   +D +  NFD G   GF+GG+ +  +QA   PI GT+ PPGTP+WG  W
Sbjct: 363 SFATAGATGEMFNDISPGNFDDGVKLGFIGGAKIHSSQASGAPI-GTALPPGTPSWGRGW 421

Query: 426 KKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIKMNRFM 485
           K+   D+Y H + +       SYRG++LDLDP Y+D +G PLLRMTFDW++N++K+ R++
Sbjct: 422 KEGMIDWYDHSMKISITTTCMSYRGHFLDLDPNYKDPWGQPLLRMTFDWRQNELKLQRYL 481

Query: 486 VEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRYLQSWD 545
            + + KI++ +NP  ++     +  H++   Y +TH  GGAIMG  P+ SALN+YLQSWD
Sbjct: 482 RDIVLKISKELNPDHMSESFLALDSHWDITKYVSTHNVGGAIMGDSPRDSALNKYLQSWD 541

Query: 546 VHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           VHNVFVPG +AFPQ    NPT  + A+T  +A AI+ QYLKNPGPLVQA
Sbjct: 542 VHNVFVPGGNAFPQNFQANPTATIGAITLMAAHAIKTQYLKNPGPLVQA 590


Lambda     K      H
   0.318    0.136    0.423 

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: 1276
Number of extensions: 70
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: 594
Length of database: 590
Length adjustment: 37
Effective length of query: 557
Effective length of database: 553
Effective search space:   308021
Effective search space used:   308021
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: 53 (25.0 bits)

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

Downloads

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

Related tools

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