GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pantoea rwandensis LMG 26275

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_084936596.1 HA51_RS21490 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_002095475.1:WP_084936596.1
          Length = 387

 Score =  313 bits (801), Expect = 1e-89
 Identities = 183/404 (45%), Positives = 259/404 (64%), Gaps = 23/404 (5%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DL GKRV++R D NVPVK+G V  D RIRA+LPTI+ AL+QGAKV++ SHL
Sbjct: 1   MSVIKMTDLDLAGKRVLIRADLNVPVKEGKVTSDARIRASLPTIEAALKQGAKVMVTSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +GE + EFSL PV   L E L          +  +  + V E+  GE+++LEN RF
Sbjct: 61  GRPTEGEYNEEFSLLPVVNYLKEKLNG----TTVTLAKDYLEGV-EVGAGELVVLENVRF 115

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
           + GE K++  L+K +A+L D+ V DAFGTAHRA AS  G+ +F P + AG L+  E++ L
Sbjct: 116 NKGEKKDEETLSKKYAALCDVFVMDAFGTAHRAQASTHGVGKFAPIACAGPLLSAELEAL 175

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            KV  NPE+P V V+GG+KVS K  V+ +L++ AD +++GG +  TF+ A+   VG S  
Sbjct: 176 GKVMSNPERPLVAVVGGSKVSTKFDVLQSLVKIADTVIVGGGIANTFV-AIDNNVGKSLY 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIE---PGVEKKVVRIDDGIPEGWMGLD 295
           E D ++ AK+L +   E G+ +  P D+ +  +     P   KKV  + D        +D
Sbjct: 235 EPDFVEAAKKLRD---EHGIPV--PTDSRVGTEFSETAPSTVKKVSEVADNEEI----MD 285

Query: 296 IGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGD 355
            G ET       L DAKT++WNGP+GVFE  +F +GT+ VA AIA   +  A +V GGGD
Sbjct: 286 FGDETALAMAALLKDAKTILWNGPVGVFEFPNFRKGTEIVANAIA---DSDAFSVAGGGD 342

Query: 356 SAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399
           + AA++ FGLEDK S++STGGGA LEF+EGK+LP +A + ++ K
Sbjct: 343 TLAAIDLFGLEDKISYISTGGGAFLEFVEGKKLPAVAMLEERAK 386


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: 635
Number of extensions: 35
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: 387
Length adjustment: 34
Effective length of query: 620
Effective length of database: 353
Effective search space:   218860
Effective search space used:   218860
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 24 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