GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Kocuria flava HO-9041

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_058858667.1 AS188_RS09630 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_001482365.1:WP_058858667.1
          Length = 407

 Score =  354 bits (908), Expect = e-102
 Identities = 190/394 (48%), Positives = 260/394 (65%), Gaps = 15/394 (3%)

Query: 13  GKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPEFS 72
           G+RV++R D NVP+    V DD R+RA+LP I+     GA+VI+++HLGRPKG+  P++S
Sbjct: 15  GRRVLVRSDLNVPLDGVTVTDDGRVRASLPVIEKLAHAGARVIVMAHLGRPKGQVDPKYS 74

Query: 73  LAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDPELA 131
           +AP  +RL+EL    V+    VVG + +     L +GEVL+LEN RF P ET K+D E  
Sbjct: 75  IAPAGQRLAELADVPVRIATDVVGQDARDKAAALADGEVLVLENVRFDPRETSKDDAERG 134

Query: 132 KFWASLADI------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNP 185
                LA +      +V DAFG  HR HAS   IA  +P+  G L+ +E++ L+KV  +P
Sbjct: 135 ALADELAALTGENGAYVGDAFGAVHRKHASVYDIAHRLPAYQGDLVRRELEVLTKVVQDP 194

Query: 186 EKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDL 245
           E+P+VVV+GG+KVSDK+ VI NL+ +AD +LIGG M+FTFL A G  VG S +EED+++ 
Sbjct: 195 ERPFVVVMGGSKVSDKLAVIDNLIGRADALLIGGGMVFTFLAAQGHRVGGSLLEEDQLET 254

Query: 246 AKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDD----GIPEGWMGLDIGPETI 301
            K  LE+A + G EIVLPVD V A++       +   ++D     I    +GLDIGP + 
Sbjct: 255 VKGYLERAADAGTEIVLPVDVVYAERFAADAPHETRPVEDIVGGQIGASGLGLDIGPASA 314

Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361
            LF  ++  A+TV WNGPMGVFE+D FA GT+ VA AI A     A++V+GGGDSA+AV 
Sbjct: 315 ALFADRIKAARTVFWNGPMGVFEMDAFAAGTRAVAEAIVA---SEAMSVIGGGDSASAVR 371

Query: 362 KFGLED-KFSHVSTGGGASLEFLEGKELPGIASI 394
             G  D +F H+STGGGASLEF+EGKELPG+ ++
Sbjct: 372 NLGFTDEQFGHISTGGGASLEFIEGKELPGVVAL 405


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: 681
Number of extensions: 29
Number of successful extensions: 5
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: 407
Length adjustment: 35
Effective length of query: 619
Effective length of database: 372
Effective search space:   230268
Effective search space used:   230268
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