GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF2967 HP15_2911 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Marino:GFF2967
          Length = 386

 Score =  343 bits (879), Expect = 1e-98
 Identities = 195/399 (48%), Positives = 266/399 (66%), Gaps = 19/399 (4%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           +++MT  D++L GKRV++R D NVPVKDG V  D RIRA+LPTIK A + GAKV+L+SHL
Sbjct: 3   IKRMT--DLNLAGKRVLIREDLNVPVKDGKVSSDARIRASLPTIKAAKDAGAKVMLMSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +G      S+ PVA  L+++LG+EV+ +   + D V     E+ +GEV+L EN RF
Sbjct: 61  GRPEEGVYDEASSMKPVADHLTKVLGQEVRLIKDYL-DGV-----EVADGEVVLFENVRF 114

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
           + GE K++ +LAK +A+L D++V DAFGTAHRA AS  G+A+F P + AG L+  E++ L
Sbjct: 115 NKGEKKDNEDLAKKYAALCDVYVMDAFGTAHRAQASTHGVARFAPEACAGPLLAAELEAL 174

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K   NP KP V ++GG+KVS K+ V+  L +  D I++GG +  TFL A G  VG S  
Sbjct: 175 GKALDNPAKPVVAIVGGSKVSTKLDVLNALEKVCDSIIVGGGIANTFLAAAGHPVGKSLC 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E D ID AKE+  +     VEI LPVD V+A +        V  I D + E  M LD+GP
Sbjct: 235 EHDLIDTAKEIASR-----VEIPLPVDVVVASEFAETATATVKNISD-VTEDDMILDVGP 288

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           ET   F + L +AKT++WNGP+GVFE D F  GTK +A AIA   E  A ++ GGGD+ A
Sbjct: 289 ETAGEFAELLKNAKTILWNGPVGVFEFDQFGNGTKALAEAIA---ESDAFSLAGGGDTVA 345

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397
           AV+K+G+ DK S++STGGGA LEF+EGK LP +A + ++
Sbjct: 346 AVDKYGVADKISYISTGGGAFLEFVEGKTLPAVAVLEER 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: 619
Number of extensions: 38
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: 386
Length adjustment: 34
Effective length of query: 620
Effective length of database: 352
Effective search space:   218240
Effective search space used:   218240
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