GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Desulfovibrio vulgaris Miyazaki F

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 8499899 DvMF_0664 Orn/DAP/Arg decarboxylase 2 (RefSeq)

Query= curated2:O27390
         (428 letters)



>FitnessBrowser__Miya:8499899
          Length = 474

 Score =  142 bits (359), Expect = 2e-38
 Identities = 119/442 (26%), Positives = 192/442 (43%), Gaps = 46/442 (10%)

Query: 6   EVNDKGHLL-IGGADAVELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACK 64
           +V D+G +L +GG     LA +YGTPL V+D   +R   + +  A         + Y+ K
Sbjct: 31  DVTDEGGVLAVGGMPCTRLARDYGTPLLVVDAAALRRRVQDVQAALDEVLPGAMLAYSYK 90

Query: 65  ANTNLAVMRILEEEGSGIDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVR 124
            N    ++R+L + G G + +SP E + +   G D  +++Y G +   + +  A+  G  
Sbjct: 91  TNCIPGILRMLHDAGVGAEVISPYEYWLSESLGVDGGQVVYNGVDKSRESIARAVARGTL 150

Query: 125 INVDSRSQLLRLSEIAPE-------GLRISFRVNPLVGAGHHEHCITGGEMSKFGVMERE 177
           +N+DSR ++  +   A E       GLR++   +   G         G +++       +
Sbjct: 151 VNIDSRDEVDVVLAAAREQRRTARVGLRLALNRSAQFGLDPE-----GDDLAHVVRNCLD 205

Query: 178 APEVYRMAMDLGFEPVGIHAHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFG 237
           AP+      DL    V +H ++ S           +   +D+   +    GV    +D G
Sbjct: 206 APD----HADL----VALHFNVTSNARHSGYHARCLSRALDVMSWLAREHGVRIRLLDVG 257

Query: 238 GGLGI--------------------PYTPEEEPL-DIDEFASKITGLFKDKLSEYGLGRP 276
           GG G+                    P     +P  D   +   +    +   ++  L  P
Sbjct: 258 GGFGVETSKNMSGAEYGLYRLFGVQPGAAWMDPFQDFRLYLRDLADTLRAFCAQNDLPVP 317

Query: 277 MMCLEPGRYIVGDASYLLTRVNTIKE--SYRKFAGVDAGFNTLLRPAMYGSYHHILVAER 334
            +C+EPGR +   A  LLT+V  +KE      FA  DAG  +   P  +  +H   +A  
Sbjct: 318 GVCIEPGRLLTSKAELLLTQVKAVKERPGAEPFAITDAGRLSQAFPCDF-EWHEAFLASD 376

Query: 335 PLDEPSEKMDVAGNVCESGDLFARDRQLPEINEGDVLAIMNAGAYSFSMSSQYNSRPRPA 394
               PS    V G VC   D   R + LPE+  GDVLA+M+AGAY FS  +   + PR A
Sbjct: 377 LRRPPSRPYTVTGRVCTRSDWLYRGKLLPELATGDVLAVMDAGAY-FSSYAMNFAFPRAA 435

Query: 395 EVLVREGKVDVVRERETFSDLL 416
            V V +G+  V+R RE F  L+
Sbjct: 436 VVAVEDGRARVLRRREDFRHLV 457


Lambda     K      H
   0.320    0.140    0.408 

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: 572
Number of extensions: 32
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 428
Length of database: 474
Length adjustment: 33
Effective length of query: 395
Effective length of database: 441
Effective search space:   174195
Effective search space used:   174195
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 Aug 03 2021. The underlying query database was built on Aug 03 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