GapMind for catabolism of small carbon sources

 

Alignments 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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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