Aligments for a candidate for adh in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Desulfovibrio vulgaris Miyazaki F

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

Query= CharProtDB::CH_018413
         (862 letters)



>FitnessBrowser__Miya:8501604
          Length = 904

 Score =  962 bits (2488), Expect = 0.0
 Identities = 479/859 (55%), Positives = 637/859 (74%), Gaps = 8/859 (0%)

Query: 9   LDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLVEDKVIK 68
           +D+ +  + EAQ+ F+ ++Q+ VD IF  AA AA   RI LA+ AV ETGMG++EDKVIK
Sbjct: 36  VDDIVTRVNEAQRAFANFTQQQVDAIFHAAAAAATAQRIHLARMAVQETGMGILEDKVIK 95

Query: 69  NHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIFKSLISL 128
           NHFA EYIYNKYKD+KTCG+I  +  YG  ++A PIGV+A IIP TNPTSTTIFK+L++L
Sbjct: 96  NHFASEYIYNKYKDDKTCGVIRDDPAYGYREVAAPIGVIAGIIPTTNPTSTTIFKALLAL 155

Query: 129 KTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLMQKADIT 188
           KTRNGI F+PHPRA KST+ AA+ + +AAV +GAP  IIGW++ P+ +LT+ LMQ   + 
Sbjct: 156 KTRNGIIFAPHPRAAKSTVEAARIVHEAAVAAGAPRGIIGWVEAPTPDLTRQLMQHRGVA 215

Query: 189 L--ATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGVICAS 246
           L  ATGGP +V +AYSSGKPAIGVG GNTPV++D SA++KMAV+SIILSKT+DNG+ICAS
Sbjct: 216 LILATGGPGMVHAAYSSGKPAIGVGAGNTPVVVDASANVKMAVNSIILSKTFDNGMICAS 275

Query: 247 EQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQSAYTIAAMA 306
           EQ+VIV  +  + VK EF  RG +     E + +  V+F DG +N  IVG+SA  IAAMA
Sbjct: 276 EQAVIVEDAAADAVKAEFAARGCHFASPQEAEALAGVVFTDGRLNAAIVGRSAAEIAAMA 335

Query: 307 GIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLINLGGLGHT 366
           GI VP TT+ILI E  ++   +PFAHEKLSPVL  Y A +F  A+  A  L+ LGG GHT
Sbjct: 336 GITVPPTTKILIAERDAIDPLDPFAHEKLSPVLGFYRAPDFAAAVDMAQRLVELGGAGHT 395

Query: 367 SGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCGFWGGNS 426
           S +Y +E   R++I  F + + T RT VN+P+SQGA GD+YNF + PS TLGCG WG NS
Sbjct: 396 SVLYTNEAN-RERIVHFQNVLTTGRTLVNMPSSQGAIGDVYNFELAPSLTLGCGSWGDNS 454

Query: 427 VSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKKRAFIVTDS 486
           VSEN+G KHL+N+KTVAERRENMLWFRVP K+YFK G L+ AL+D++D  +KRAFIVTD 
Sbjct: 455 VSENIGVKHLMNVKTVAERRENMLWFRVPPKIYFKMGALRLALEDMRD--RKRAFIVTDR 512

Query: 487 DPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTIIALGGTPE 546
              +L +V  +  +LE L I F+VF+ V  + DL     A + + +F PD  IALGG   
Sbjct: 513 TMEDLGHVGKVTAVLEKLGIQFRVFSDVKPDPDLSGTYAALDSIRAFRPDMFIALGGGSP 572

Query: 547 MSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAGSGSEVTPF 606
           M +AK+MW++YE P++KFE+++++FMDIRKR++ FP LGKKA++VA+ T++G+GSEVTPF
Sbjct: 573 MDAAKIMWLMYEQPDLKFEEISLRFMDIRKRVHAFPALGKKAVMVAVPTTSGTGSEVTPF 632

Query: 607 ALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIEAYTSVYAS 666
           A++TD+ TG KY +ADYE+TP+MAIVD E +M MPK LTA+SG+DAL +++EA+TS YA+
Sbjct: 633 AVITDDATGMKYPIADYELTPDMAIVDPEFVMDMPKTLTAHSGLDALTHAVEAFTSTYAN 692

Query: 667 EYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLGLCHSMAIK 726
            +++G ALEA+RL+FKYL  AY +G  +  AREKM +A T+AGMA ANAFLG+CHSMA K
Sbjct: 693 NFSDGNALEAVRLVFKYLRRAYNDGARDVMAREKMHYAGTIAGMAFANAFLGVCHSMAHK 752

Query: 727 LSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIADYIKLG--- 783
           L +  ++P G+ANALL+  VI++NA D P KQ   PQY+YP    RYARIAD + L    
Sbjct: 753 LGAAFHMPHGLANALLLSHVIEYNATDTPTKQGLMPQYRYPFVKGRYARIADMLGLTEGC 812

Query: 784 GNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQCTGANPR 843
           G+  + KV  L+  I +LK  LN+P S+++AG+ E +F   +D ++E A DDQCTG NPR
Sbjct: 813 GDDRDRKVARLVQAIEQLKADLNVPGSLREAGIAEADFLERVDLLAEQAFDDQCTGGNPR 872

Query: 844 FPLTSEIKEMYINCFKKQP 862
           +PL +EI+E+Y+  +   P
Sbjct: 873 YPLIAEIRELYLKAYYGAP 891


Lambda     K      H
   0.317    0.134    0.378 

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: 1844
Number of extensions: 79
Number of successful extensions: 5
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: 862
Length of database: 904
Length adjustment: 43
Effective length of query: 819
Effective length of database: 861
Effective search space:   705159
Effective search space used:   705159
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 (21.6 bits)
S2: 56 (26.2 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