Aligments for a candidate for ald-dh-CoA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for ald-dh-CoA in Desulfovibrio vulgaris Miyazaki F

Align alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized)
to candidate 8501604 DvMF_2322 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= metacyc::GIO2-535-MONOMER
         (954 letters)



>FitnessBrowser__Miya:8501604
          Length = 904

 Score = 1044 bits (2699), Expect = 0.0
 Identities = 525/896 (58%), Positives = 667/896 (74%), Gaps = 14/896 (1%)

Query: 52  PKAEAAAPVAAAPATPHAEVKKERAPAT--DEALTELKALLKRAQTAQAQYSTYTQEQVD 109
           P A+ A P      TP A    + +P++    ++T +  ++ R   AQ  ++ +TQ+QVD
Sbjct: 5   PNAQGAKPAT----TPDAISLNDISPSSIAPNSIT-VDDIVTRVNEAQRAFANFTQQQVD 59

Query: 110 EIFRAAAEAANAARIPLAKMAVEETRMGVAEDKVVKNHFASEFIYNKYKHTKTCGVIEHD 169
            IF AAA AA A RI LA+MAV+ET MG+ EDKV+KNHFASE+IYNKYK  KTCGVI  D
Sbjct: 60  AIFHAAAAAATAQRIHLARMAVQETGMGILEDKVIKNHFASEYIYNKYKDDKTCGVIRDD 119

Query: 170 PAGGIQKVAEPVGVIAGIVPTTNPTSTAIFKSLLSLKTRNALVLCPHPRAAKSTIAAARI 229
           PA G ++VA P+GVIAGI+PTTNPTST IFK+LL+LKTRN ++  PHPRAAKST+ AARI
Sbjct: 120 PAYGYREVAAPIGVIAGIIPTTNPTSTTIFKALLALKTRNGIIFAPHPRAAKSTVEAARI 179

Query: 230 VRDAAVAAGAPPNIISWVETPSLPVSQALMQATEINLILATGGPAMVRAAYSSGNPSLGV 289
           V +AAVAAGAP  II WVE P+  +++ LMQ   + LILATGGP MV AAYSSG P++GV
Sbjct: 180 VHEAAVAAGAPRGIIGWVEAPTPDLTRQLMQHRGVALILATGGPGMVHAAYSSGKPAIGV 239

Query: 290 GAGNTPALIDETADVAMAVSSILLSKTFDNGVICASEQSVVVVAKAYDAVRTEFVRRGAY 349
           GAGNTP ++D +A+V MAV+SI+LSKTFDNG+ICASEQ+V+V   A DAV+ EF  RG +
Sbjct: 240 GAGNTPVVVDASANVKMAVNSIILSKTFDNGMICASEQAVIVEDAAADAVKAEFAARGCH 299

Query: 350 FLTEDDKVKVRAGVVVDGKLNPNIVGQSIPKLAALFGIKVPQGTKVLIGEVEKIGPEEAL 409
           F +  +   +   V  DG+LN  IVG+S  ++AA+ GI VP  TK+LI E + I P +  
Sbjct: 300 FASPQEAEALAGVVFTDGRLNAAIVGRSAAEIAAMAGITVPPTTKILIAERDAIDPLDPF 359

Query: 410 SQEKLCPILAMYRAPDYDHGVKMACELIMYGGAGHTSVLYTNPLNNAHIQQYQSAVKTVR 469
           + EKL P+L  YRAPD+   V MA  L+  GGAGHTSVLYTN  N   I  +Q+ + T R
Sbjct: 360 AHEKLSPVLGFYRAPDFAAAVDMAQRLVELGGAGHTSVLYTNEANRERIVHFQNVLTTGR 419

Query: 470 ILINTPASQGAIGDLYNFHLDPSLTLGCGTWGSTSVSTNVGPQHLLNIKTVTARRENMLW 529
            L+N P+SQGAIGD+YNF L PSLTLGCG+WG  SVS N+G +HL+N+KTV  RRENMLW
Sbjct: 420 TLVNMPSSQGAIGDVYNFELAPSLTLGCGSWGDNSVSENIGVKHLMNVKTVAERRENMLW 479

Query: 530 FRVPPKIYFKGGCLEVALTDLRGKSRAFIVTDKPLFDMGYADKVTHILDSINVHHQVFYH 589
           FRVPPKIYFK G L +AL D+R + RAFIVTD+ + D+G+  KVT +L+ + +  +VF  
Sbjct: 480 FRVPPKIYFKMGALRLALEDMRDRKRAFIVTDRTMEDLGHVGKVTAVLEKLGIQFRVFSD 539

Query: 590 VTPDPTLACIEAGLKEILEFKPDVIIALGGGSPMDAAKIMWLMYECPDTRFDGLAMRFMD 649
           V PDP L+   A L  I  F+PD+ IALGGGSPMDAAKIMWLMYE PD +F+ +++RFMD
Sbjct: 540 VKPDPDLSGTYAALDSIRAFRPDMFIALGGGSPMDAAKIMWLMYEQPDLKFEEISLRFMD 599

Query: 650 IRKRVYEVPELGKKATMVCIPTTSGTGSEVTPFSVVTDERLGAKYPLADYALTPSMAIVD 709
           IRKRV+  P LGKKA MV +PTTSGTGSEVTPF+V+TD+  G KYP+ADY LTP MAIVD
Sbjct: 600 IRKRVHAFPALGKKAVMVAVPTTSGTGSEVTPFAVITDDATGMKYPIADYELTPDMAIVD 659

Query: 710 PQLVLNMPKKLTAWGGIDALTHALESYVSICATDYTKGLSREAISLLFKYLPRAYANGSN 769
           P+ V++MPK LTA  G+DALTHA+E++ S  A +++ G + EA+ L+FKYL RAY +G+ 
Sbjct: 660 PEFVMDMPKTLTAHSGLDALTHAVEAFTSTYANNFSDGNALEAVRLVFKYLRRAYNDGAR 719

Query: 770 DYLAREKVHYAATIAGMAFANAFLGICHSMAHKLGAAYHVPHGLANAALISHVIRYNATD 829
           D +AREK+HYA TIAGMAFANAFLG+CHSMAHKLGAA+H+PHGLANA L+SHVI YNATD
Sbjct: 720 DVMAREKMHYAGTIAGMAFANAFLGVCHSMAHKLGAAFHMPHGLANALLLSHVIEYNATD 779

Query: 830 MPAKQAAFPQYEYPTAKQDYADLANMLGLG---GNTVDEKVIKLIEAVEELKAKVDIPPT 886
            P KQ   PQY YP  K  YA +A+MLGL    G+  D KV +L++A+E+LKA +++P +
Sbjct: 780 TPTKQGLMPQYRYPFVKGRYARIADMLGLTEGCGDDRDRKVARLVQAIEQLKADLNVPGS 839

Query: 887 IKEIFNDPKVDADFLANVDALAEDAFDDQCTGANPRYPLMADLKQLYLDA-HAAPI 941
           ++E       +ADFL  VD LAE AFDDQCTG NPRYPL+A++++LYL A + AP+
Sbjct: 840 LREA---GIAEADFLERVDLLAEQAFDDQCTGGNPRYPLIAEIRELYLKAYYGAPL 892


Lambda     K      H
   0.318    0.133    0.387 

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: 1948
Number of extensions: 72
Number of successful extensions: 3
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: 954
Length of database: 904
Length adjustment: 43
Effective length of query: 911
Effective length of database: 861
Effective search space:   784371
Effective search space used:   784371
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: 57 (26.6 bits)

This GapMind analysis is from Sep 17 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)
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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, or view the source code.

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