GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Collimonas arenae Ter10

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_061535450.1 CAter10_RS18070 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_001584165.1:WP_061535450.1
          Length = 394

 Score =  310 bits (795), Expect = 6e-89
 Identities = 174/377 (46%), Positives = 244/377 (64%), Gaps = 13/377 (3%)

Query: 18  MRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSPEFSLAP 75
           +R D NVP  D G + +DTRIRA++P I+ AL+ GA V++ SHLGRP +GE  PE SLAP
Sbjct: 20  IRADLNVPQDDAGNITEDTRIRASVPAIRQALDAGAAVMVTSHLGRPTEGEFKPEDSLAP 79

Query: 76  VAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPELAKFWA 135
           +AKRL+ELLG+ V+     V D V     ++  G+V+LLEN R + GE KN  ELA+  A
Sbjct: 80  IAKRLAELLGQPVELKQNWV-DGV-----DVAPGQVVLLENCRVNKGEKKNSDELAQKIA 133

Query: 136 SLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKPYVVVLG 194
            L DI+VNDAFGTAHRA A+  GIA+F P + AG L+  E+  L K    P +P V ++ 
Sbjct: 134 KLCDIYVNDAFGTAHRAEATTHGIAKFAPVACAGPLLAAELDALGKALNQPARPLVAIVA 193

Query: 195 GAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAK 254
           G+KVS K+ ++  L +K D +++GG +  TFL A   ++G S  E D ++ AK ++E   
Sbjct: 194 GSKVSSKLTILKALADKVDNLIVGGGIANTFLLASRLKIGKSLAEPDLVEEAKAIIEMMA 253

Query: 255 EKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTV 314
           ++G  + +PVD V A++  P    ++  + D + E  + LDIGP+T      +++ A TV
Sbjct: 254 KRGASVPIPVDVVCAKEFSPTAVAQIKDVGD-VAEDDLILDIGPKTAATLAAQIAQAGTV 312

Query: 315 VWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVST 374
           VWNGP+GVFE D F EGTK +ALAIA      A ++ GGGD+ AA+ K+ + DK  ++ST
Sbjct: 313 VWNGPVGVFEFDQFGEGTKTLALAIA---NSKAFSIAGGGDTLAAIAKYNITDKIGYIST 369

Query: 375 GGGASLEFLEGKELPGI 391
           GGGA LEFLEGK LP +
Sbjct: 370 GGGAFLEFLEGKTLPAV 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: 592
Number of extensions: 30
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: 394
Length adjustment: 34
Effective length of query: 620
Effective length of database: 360
Effective search space:   223200
Effective search space used:   223200
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