GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Desulfovibrio vulgaris Miyazaki F

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 8500217 DvMF_0975 phosphoglycerate kinase (RefSeq)

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Miya:8500217
          Length = 393

 Score =  328 bits (842), Expect = 2e-94
 Identities = 182/399 (45%), Positives = 258/399 (64%), Gaps = 12/399 (3%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DLKGKRV++R D NVP+KDG V  D RIRAALP+I+ AL+ GA+V+L+SHL
Sbjct: 1   MAVLKMTDLDLKGKRVLLREDLNVPLKDGKVTSDKRIRAALPSIEMALKAGARVLLVSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +GE  P FSLAPVA+ LS  LG +V  V   + D +     E+ EG+ +L EN RF
Sbjct: 61  GRPTEGEFDPAFSLAPVAEHLSRALGFQVPLVRDYI-DGI-----EVAEGQCVLCENVRF 114

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
             GE K+D  L +  A+L DI V DAFG AHRA AS     +F   + AG L+  E+  L
Sbjct: 115 LKGEKKDDEALGRKLAALCDIFVMDAFGAAHRAQASTHAAVRFAKVACAGPLLAAELDAL 174

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
           S+    P KP V ++GG+KVS K+ ++  L +K DR+++GG +   F+KA G EVG S  
Sbjct: 175 SRALDAPAKPMVGIIGGSKVSTKLTLLDTLSKKVDRLIVGGGIANNFIKAAGHEVGRSLY 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E + +D A  L+  A+  G EI +PVD V+  +        V ++ +  P+  M LDIGP
Sbjct: 235 EPELVDEAARLMAAARAAGGEIPVPVDVVVGPEFADSAPATVRKVSEVKPDE-MILDIGP 293

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           ET +L++  L  A T+VWNGP+G FE++ F +GTK + +A+A   +  A ++ GGGD+ A
Sbjct: 294 ETAKLYRDILMQAGTIVWNGPVGAFEVEQFGQGTKALCMAVA---DSPAFSLAGGGDTVA 350

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397
           A+ K+G+ D+ S++STGGGA LEFLEGK LP +A + ++
Sbjct: 351 AIEKYGVVDRISYMSTGGGAFLEFLEGKTLPAVAVLEER 389


Lambda     K      H
   0.317    0.137    0.386 

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: 633
Number of extensions: 38
Number of successful extensions: 6
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: 654
Length of database: 393
Length adjustment: 34
Effective length of query: 620
Effective length of database: 359
Effective search space:   222580
Effective search space used:   222580
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: 52 (24.6 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