GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Pseudomonas fluorescens FW300-N2C3

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate AO356_19620 AO356_19620 glyoxylate carboligase

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19620
          Length = 591

 Score =  321 bits (823), Expect = 5e-92
 Identities = 191/581 (32%), Positives = 314/581 (54%), Gaps = 43/581 (7%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH-SDLIHLLTRHEQAAAHAADGYAR 59
           M   EA +  +  E V+  FG PG A+ P Y AL     + H+L RH + A+H A+GY R
Sbjct: 4   MRAIEAAVLVMRREGVDTAFGIPGAAINPLYSALQKVGGIDHVLARHVEGASHMAEGYTR 63

Query: 60  A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
             +G +GVCIGTSGP  T++VTG+ +A +DS P++ +TGQ P   +  + FQ +D   + 
Sbjct: 64  TKAGNIGVCIGTSGPAGTDMVTGLYSASADSIPILCITGQAPRARMHKEDFQAVDITSIV 123

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKHPIPSK 176
            P+ K    + +  Q+P  F+ AF   ++GRPGPV IDLP DVQ  E+E DID       
Sbjct: 124 KPVTKWATTVLEPGQVPYAFQKAFFEMRSGRPGPVLIDLPFDVQMAEIEFDID------- 176

Query: 177 VKLIGYNPTTIGHPR----QIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232
                Y P  +  P     QI+KA+ ++  A+RP+++AGGG++ + A++ L++  EL  I
Sbjct: 177 ----AYQPLPLAKPAANRVQIEKALAMLNQAERPLLVAGGGIINADASDLLVEFAELTGI 232

Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSF 291
           PV  TLMG G I ++HP  +GMVG+  + +  N  L +SDV++ +G R+++R TG +  +
Sbjct: 233 PVIPTLMGWGTIPDDHPQMVGMVGLQTSHRYGNATLLKSDVVLGVGNRWANRHTGSVDVY 292

Query: 292 ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQ 351
                 IH+DI+P +IG+    D+ IV DA   L   I+     + ++ +     +N S 
Sbjct: 293 TEGRTFIHVDIEPTQIGRVFTPDLGIVSDAASALTVFIE-----VAREWQAAGKLKNRSA 347

Query: 352 WIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAH 411
           W+++    K S      +D++P+KPQ++ +E+  V       K+T   + +G +Q+  A 
Sbjct: 348 WLQDCQQRKASLQRKTHFDNVPVKPQRVYEEMNQV-----FGKDTCYVSTIGLSQIAGAQ 402

Query: 412 YFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEY 471
           +     PR +++ G  G +G+  P+A+G   A P  KV+ ++GD  F    +EL   A++
Sbjct: 403 FLHVYKPRHWINCGQAGPLGWTIPAALGVVKADPSRKVVALSGDYDFQFMIEELAVGAQF 462

Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKA 522
            +P +  + +N  LG++ Q Q  F       ++F         G   D + +AE  G KA
Sbjct: 463 KLPYIHVVVNNSYLGLIRQAQRGFDMDYCVQLSFDNLNAPELNGYGVDHVAVAEGLGCKA 522

Query: 523 RRIESPNEINEALKEAINCDE----PYLLDFAIDPSSALSM 559
            R+  P  I  AL++A    E    P +++  ++  + +SM
Sbjct: 523 LRVFEPAGIQPALRQAQAMIEEFKVPVIVEIILERVTNISM 563


Lambda     K      H
   0.319    0.137    0.405 

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: 804
Number of extensions: 39
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: 599
Length of database: 591
Length adjustment: 37
Effective length of query: 562
Effective length of database: 554
Effective search space:   311348
Effective search space used:   311348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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