GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Hydrogenovibrio halophilus DSM 15072

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_028485251.1 A377_RS0103985 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000384235.1:WP_028485251.1
          Length = 393

 Score =  334 bits (857), Expect = 4e-96
 Identities = 179/393 (45%), Positives = 261/393 (66%), Gaps = 11/393 (2%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DL GKRV++R D NVPVK+G V  D RIRA+LPT+K A E GAKV+++SHL
Sbjct: 1   MSVLKMSDLDLAGKRVLIREDLNVPVKNGKVTSDARIRASLPTMKMAAEAGAKVMIMSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +GE   E S+APVA  LSE LGK+V+ +   +  +V     ++  GE++LLEN RF
Sbjct: 61  GRPTEGEFDQESSMAPVAADLSEKLGKDVRLIKDYLDGDV-----DVAAGEIVLLENVRF 115

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
           + GE KND  L+K +A+L DI+V DAFGTAHRA AS  G  ++ P + AG L+  E++ L
Sbjct: 116 NVGEKKNDVALSKKYAALCDIYVMDAFGTAHRAQASTHGAGEYAPVACAGPLLAAELEAL 175

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K  + P++P V ++GG+KVS K+ V+ +L EK D++++GG +  TF++A G  VG+S  
Sbjct: 176 GKALHEPKRPMVAIVGGSKVSTKLTVLESLSEKVDQLVVGGGIANTFIEAAGHNVGNSLS 235

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E D +   K+L E  + +G  I L  D V  ++     + +   + + + +  M  DIGP
Sbjct: 236 ETDLVPTCKKLNEIMESRGAAIPLASDVVCGKEFSENAKAETKPVAEVVDDD-MIFDIGP 294

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           ++     + + +A TVVWNGP+GVFE D F EGTK +++AIA   E  A ++ GGGD+ A
Sbjct: 295 DSAAELAKIIKEAGTVVWNGPVGVFEFDQFGEGTKAISMAIA---ESDAFSIAGGGDTLA 351

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGI 391
           A++K+ + DK S++STGGGA LEFLEGK+LP +
Sbjct: 352 AIDKYDIADKVSYISTGGGAFLEFLEGKKLPAV 384


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: 596
Number of extensions: 40
Number of successful extensions: 7
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 Apr 09 2024. 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