GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Caulobacter crescentus NA1000

Align Uncharacterized aminotransferase MJ0959; EC 2.6.1.- (characterized, see rationale)
to candidate CCNA_02687 CCNA_02687 serine-pyruvate aminotransferase

Query= uniprot:Y959_METJA
         (385 letters)



>FitnessBrowser__Caulo:CCNA_02687
          Length = 426

 Score =  197 bits (501), Expect = 5e-55
 Identities = 126/400 (31%), Positives = 203/400 (50%), Gaps = 21/400 (5%)

Query: 2   KIDAVKKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TF 60
           ++D   +LLM PGP  V P VL AM++ ++G    +++  + + +   + VF T+N  TF
Sbjct: 26  ELDHPARLLMGPGPINVHPRVLRAMSVQLLGQFDPEFTGYMNEVMALYRGVFQTQNRWTF 85

Query: 61  LITGSGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEP 120
            I G+  A ++ A+ + ++ GD V+ +  G FG   A I +    +   ++  WG + +P
Sbjct: 86  TIDGTSRAGIEAALVSTLQPGDDVVVVNAGRFGLLLAEIAERCDAKVTFVEASWGAVVDP 145

Query: 121 EAVKEILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNV 180
           +AV++ + +    + V  VH +TST    P+ EIG + + + AL  VD  ++L G  V V
Sbjct: 146 QAVEDAVKRVKP-RLVACVHGDTSTTMAQPLGEIGAICRAHGALMYVDATATLSGMDVPV 204

Query: 181 DKFHIDICVTGSQKCLAAPPGLAAITVSEKAWEVI--KKNDDK---------------VG 223
           D +  DI   G QKCL  P G A IT+S++A E I  +++ +K                 
Sbjct: 205 DAWGADIVTAGLQKCLGGPSGSAPITISDQAAEHIFSRRHVEKGLAGTGGAAGAGRRIAS 264

Query: 224 FYLDLLAYKKYYEEKKQTPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGL 283
            Y DL     Y+ EK+   +T    + +A      LVLEEG+  R  RH +   A  AGL
Sbjct: 265 NYFDLAMIMDYWSEKRLNHHTECAPMLFAARECARLVLEEGLPARFDRHAQAGAAMTAGL 324

Query: 284 EAMGIELFAKERARSVTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGH 343
           EAMG+ ++  +  +   VT    P+G++  + +  +   + I +      L GKI+RIG 
Sbjct: 325 EAMGLSIYGDKAHKMTNVTGIWVPKGVDYDRVKARMRTDFEIEIGSAFGPLTGKIWRIGT 384

Query: 344 MGICGEKE-VLATLACVELALKELGFEVKE-SGVEVAKEV 381
           MG+   K  VL TLA  E  L+  GF     +GV+ A +V
Sbjct: 385 MGVNARKHAVLQTLAAFEAVLRWEGFSAPAGAGVDAAAKV 424


Lambda     K      H
   0.316    0.135    0.379 

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: 351
Number of extensions: 16
Number of successful extensions: 4
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: 385
Length of database: 426
Length adjustment: 31
Effective length of query: 354
Effective length of database: 395
Effective search space:   139830
Effective search space used:   139830
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: 50 (23.9 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