GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Pseudomonas stutzeri RCH2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF329 Psest_0330 3-phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__psRCH2:GFF329
          Length = 386

 Score =  325 bits (834), Expect = 2e-93
 Identities = 184/393 (46%), Positives = 258/393 (65%), Gaps = 17/393 (4%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60
           M  + + D+DL+GKRV++R D NVPVKDG V+ D RI A+LPTIK ALE+GA V++ SHL
Sbjct: 1   MTVLKMTDLDLQGKRVLIREDLNVPVKDGAVKSDARILASLPTIKLALEKGAAVLVCSHL 60

Query: 61  GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           GRP +G  S E SL PVA  LS+ LG+EV  +   + D V     E++ GE++LLEN RF
Sbjct: 61  GRPEEGVYSEEDSLKPVADYLSKALGREVPLIKDYL-DGV-----EVQPGELVLLENVRF 114

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178
           + GE KN  ELA+ +A+L D+ V DAFGTAHRA  S  G+A+F   + AG L+  E+  L
Sbjct: 115 NKGEKKNTDELAQKYAALCDVFVMDAFGTAHRAQGSTHGVAKFAKVACAGPLLAAELDAL 174

Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238
            K    P KP V ++ G+KVS K+ V+T+L +  D++++GG +  TFL A G  VG S  
Sbjct: 175 GKALKTPAKPMVAIVAGSKVSTKLDVLTSLADVCDQLIVGGGIANTFLAAAGYNVGKSLH 234

Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298
           E D +D AK +  K     V + LPVD V+A++     +  V  I D + +  M LDIGP
Sbjct: 235 EADLLDTAKAIAAK-----VAVPLPVDVVVAKEFAETADATVKAIAD-VADDDMILDIGP 288

Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358
           +T  +F + L  ++T++WNGP+GVFE D F  GTK +A AIA   +  A ++ GGGD+ A
Sbjct: 289 KTAAMFGEMLKSSQTILWNGPVGVFEFDQFGNGTKVLAQAIA---QSPAFSIAGGGDTLA 345

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGI 391
           A++K+G+ ++ S++STGGGA LEF+EGK LP +
Sbjct: 346 AIDKYGVAEQISYISTGGGAFLEFVEGKVLPAV 378


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: 582
Number of extensions: 33
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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