GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Desulfovibrio vulgaris Miyazaki F

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 8501786 DvMF_2502 glutamate-1-semialdehyde aminotransferase (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__Miya:8501786
          Length = 425

 Score =  150 bits (378), Expect = 9e-41
 Identities = 122/407 (29%), Positives = 188/407 (46%), Gaps = 34/407 (8%)

Query: 1   MSKTNADLMARRTAAVPRGVGQ---------IHPIFAESAKNATVTDVEGREFIDFAGGI 51
           M   + +L  R    +P GV             P+F   AK + +T V+G  F+D+    
Sbjct: 1   MDHRSKELFERAQQLIPGGVNSPVRACLGVDSDPLFVAHAKGSHLTTVDGTSFVDYVQSW 60

Query: 52  AVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTT 111
             +  GH HP + +A+   +++ T         E  V L E +   +PG   +   +V +
Sbjct: 61  GPMLLGHAHPVVASAIHAAVDRGTS---YGAPCEDEVVLAEAVIDALPG--VEMVRMVNS 115

Query: 112 GSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPG--GIFR 169
           G+EA  +A+++AR  TGR  V+ F G YHG     L   G  V   +    +PG  G+  
Sbjct: 116 GTEATMSALRLARGVTGRNKVVKFVGCYHGHADAFLASAGSGVATLS----IPGTPGVPE 171

Query: 170 ALYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRAL 229
           A   + L  ++  + + ++  +F      +DIAAII+EPV G  G  +    F++ LR L
Sbjct: 172 ATVRDTL--LAPYNDLTAVAELFT--LHGKDIAAIIVEPVAGNMGLVLPMNGFLQGLRDL 227

Query: 230 CDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDA 289
           C +HG LLI DEV TG  R     A ++  +  DLTT  K I GG P+    G+A+ M  
Sbjct: 228 CTEHGALLIFDEVITGF-RVNYGGAQKRFDITPDLTTLGKIIGGGLPVGAYGGRADLMRR 286

Query: 290 IAPGG---LGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVI 346
           IAP G     GT +G+P+A AA +A +   ++    D  +A    L   L+AI     V 
Sbjct: 287 IAPCGEVYQAGTLSGNPLAMAAGIATLAELKKSD-YDALEARVAALATELQAILAAKGVP 345

Query: 347 GDVRALGAMIAV-----ELFENGDSHKPNAAAVAQVVAKARDKGLIL 388
             V  + +M  V      + +   +   NAA       + RDKG+ L
Sbjct: 346 VRVNTIASMFTVFFTDQPVTDFASAKTANAALYTSYYKQMRDKGIYL 392


Lambda     K      H
   0.320    0.137    0.395 

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: 426
Number of extensions: 30
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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