GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Dinoroseobacter shibae DFL-12

Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate 3607536 Dshi_0948 L-lactate dehydrogenase (cytochrome) (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_1623
         (390 letters)



>FitnessBrowser__Dino:3607536
          Length = 390

 Score =  508 bits (1308), Expect = e-148
 Identities = 254/378 (67%), Positives = 308/378 (81%), Gaps = 4/378 (1%)

Query: 7   ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66
           IT IEDL+ I +RRVP+MFYDYA+SGS+TE T+R N SDF  +KLRQR+A++M+ RST+T
Sbjct: 4   ITEIEDLKRIYKRRVPKMFYDYAESGSWTEQTFRENSSDFDLLKLRQRIAMDMDNRSTKT 63

Query: 67  TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126
           TMVGQ+VAMPVA+AP GLTGMQHADGEI  A+AA+ FG+PFTLSTMSICSIED+A HT  
Sbjct: 64  TMVGQEVAMPVALAPVGLTGMQHADGEIKAARAAEKFGVPFTLSTMSICSIEDVAAHT-E 122

Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186
            PFWFQVY ++D DF++RL DRAK A CSAL +T+DLQ+LGQRH+D+KNGLSAPPK T A
Sbjct: 123 TPFWFQVYTLKDDDFMKRLFDRAKEAKCSALVITVDLQLLGQRHRDLKNGLSAPPKLTPA 182

Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246
           ++ N+ TK +W LGMLGTKRR FGNIVGHAKGV D SSLSSWTAE FD  L+W  ++  +
Sbjct: 183 SIANMMTKVQWGLGMLGTKRRFFGNIVGHAKGVTDPSSLSSWTAEAFDQSLDWERIKQFR 242

Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306
             W G +ILKGI+D EDA++A+N GADA++ SNHGGRQLDGA SSI  LP I DAV   G
Sbjct: 243 SWWDGPVILKGILDPEDAKMALNVGADAIVCSNHGGRQLDGALSSIRMLPQIMDAV---G 299

Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366
             IEV +D GIRSGQDVLKA ALGA+GT+IGR++ YGLGA GEAGVTRAL++I KELD++
Sbjct: 300 DKIEVHLDSGIRSGQDVLKAVALGARGTMIGRAWTYGLGAMGEAGVTRALEVIHKELDLS 359

Query: 367 MAFCGHTNINTVDRSILL 384
           M  CG  ++  +D S LL
Sbjct: 360 MGLCGRRSVEDLDASNLL 377


Lambda     K      H
   0.320    0.137    0.412 

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: 488
Number of extensions: 16
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: 390
Length of database: 390
Length adjustment: 31
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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: 50 (23.9 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