GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Desulfovibrio vulgaris Miyazaki F

Align Lactaldehyde reductase (characterized, see rationale)
to candidate 8501604 DvMF_2322 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= uniprot:Q8A199
         (384 letters)



>FitnessBrowser__Miya:8501604
          Length = 904

 Score =  232 bits (591), Expect = 4e-65
 Identities = 145/388 (37%), Positives = 213/388 (54%), Gaps = 31/388 (7%)

Query: 27  RGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQNGVAAYKASG 86
           R  K+AF VTD+ +   G   ++  V +   I + ++SDVK +P ++     + + +A  
Sbjct: 501 RDRKRAFIVTDRTMEDLGHVGKVTAVLEKLGIQFRVFSDVKPDPDLSGTYAALDSIRAFR 560

Query: 87  ADFIVALGGGSSIDTAKGIGIVVNNPD---------FADVKSLEGVADTKHKAVPTFALP 137
            D  +ALGGGS +D AK + ++   PD         F D++          K     A+P
Sbjct: 561 PDMFIALGGGSPMDAAKIMWLMYEQPDLKFEEISLRFMDIRKRVHAFPALGKKAVMVAVP 620

Query: 138 TTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALT 197
           TT+GT +EVT   VI D+    K    D    P +AIVDPE +  MPK LTA +G+DALT
Sbjct: 621 TTSGTGSEVTPFAVITDDATGMKYPIADYELTPDMAIVDPEFVMDMPKTLTAHSGLDALT 680

Query: 198 HAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNG-KDTVAREAMSQAQYIAGMGFSN 256
           HA+E++ +  A   SD   L+A+ ++ + L+ A ++G +D +ARE M  A  IAGM F+N
Sbjct: 681 HAVEAFTSTYANNFSDGNALEAVRLVFKYLRRAYNDGARDVMAREKMHYAGTIAGMAFAN 740

Query: 257 VGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNA-ESPAAP-------------KYI 302
             LG+ HSMAH LGA +  PHG+ANALLL +V+EYNA ++P                +Y 
Sbjct: 741 AFLGVCHSMAHKLGAAFHMPHGLANALLLSHVIEYNATDTPTKQGLMPQYRYPFVKGRYA 800

Query: 303 HIAKAMGVNTDGMTETEGVKAA--IEAVKALSLSIGIPQKLHEINVKEED----IPALAV 356
            IA  +G+ T+G  +    K A  ++A++ L   + +P  L E  + E D    +  LA 
Sbjct: 801 RIADMLGL-TEGCGDDRDRKVARLVQAIEQLKADLNVPGSLREAGIAEADFLERVDLLAE 859

Query: 357 AAFNDVCTGGNPRPTSVAEIEVLYRKAF 384
            AF+D CTGGNPR   +AEI  LY KA+
Sbjct: 860 QAFDDQCTGGNPRYPLIAEIRELYLKAY 887


Lambda     K      H
   0.317    0.133    0.379 

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: 883
Number of extensions: 38
Number of successful extensions: 4
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: 384
Length of database: 904
Length adjustment: 37
Effective length of query: 347
Effective length of database: 867
Effective search space:   300849
Effective search space used:   300849
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.

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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