GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dyella japonica UNC79MFTsu3.2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate N515DRAFT_4291 N515DRAFT_4291 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4291
          Length = 393

 Score =  329 bits (844), Expect = 1e-94
 Identities = 176/393 (44%), Positives = 261/393 (66%), Gaps = 12/393 (3%)

Query: 4   MTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           + + D+DL+GKRV++R D NVP++DG +    R+ A+LPTIK A + GA+V+++SHLGRP
Sbjct: 5   LRMSDLDLRGKRVLIREDLNVPIEDGRITSTQRLDASLPTIKAARDAGARVMVISHLGRP 64

Query: 64  K-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122
           K G+   E SLAPVAK L + LG  V+ +   +G        ++ EGEV++LEN R + G
Sbjct: 65  KEGQFDAESSLAPVAKWLGDKLGTPVRLIADYLGGV------DVAEGEVVVLENCRMNVG 118

Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKV 181
           E K+D  L+K +A+L DI V DAFGTAHRA AS  G+ ++ P + AG L+  E+  L K 
Sbjct: 119 EGKDDEALSKKYAALCDIFVMDAFGTAHRAQASTHGVIKYAPVAAAGPLLSAELDALGKA 178

Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241
             +P  P + ++ G+KVS K+ ++ NL+ K D++++GG +  TF+ A G  VG+S  E D
Sbjct: 179 LEHPAHPLLAIVAGSKVSTKLTLLENLIGKVDQLIVGGGIANTFIAAAGYGVGNSLYEPD 238

Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301
            +D AK+++  AK +G E+ +PVD V+A +        V  +D  + +G M LDIGP+T 
Sbjct: 239 LLDAAKKVIADAKRRGAEVPMPVDVVVAPEFSAHAPATVKPVDQ-VKDGEMILDIGPQTA 297

Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361
           + +   ++ A TVVWNGP+GVFE D F +GT+ +A A+A+     A ++ GGGD+ AAV 
Sbjct: 298 KNYAALIAKAGTVVWNGPVGVFEFDAFGKGTETLARAVAS---SDAFSIAGGGDTLAAVE 354

Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           K+G+E   S++STGGGA LEFLEGKELP +A++
Sbjct: 355 KYGIEKDVSYISTGGGAFLEFLEGKELPAVAAL 387


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: 639
Number of extensions: 40
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 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