GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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