GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Acidovorax sp. GW101-3H11

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Ac3H11_549 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_549
          Length = 458

 Score =  276 bits (705), Expect = 1e-78
 Identities = 173/426 (40%), Positives = 229/426 (53%), Gaps = 49/426 (11%)

Query: 15  LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPT 65
           + + TLA+H G SPDP+T AV  PIY T  YA  S  +H          G  Y+R  NPT
Sbjct: 32  MKIETLAVHAGYSPDPTTKAVAVPIYQTVAYAFDS-AQHGADLFDLKVPGNIYTRIMNPT 90

Query: 66  RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124
               E+ VAALEGG  A A ASGMAA T  +  + +AG ++V+   LYGGT+ LF     
Sbjct: 91  TDVLEKRVAALEGGIAALAVASGMAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLP 150

Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184
           +  G+   F D  DPA+F   I A TK ++IE+  NP+  + DIAAIA +A  HG+  +V
Sbjct: 151 QQ-GITTRFADPRDPASFAQHIDARTKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIV 209

Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV-------------------- 224
           DNT  SP L RP+  GAD+VVHS TKYL GH + VGG  V                    
Sbjct: 210 DNTVPSPYLLRPIEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEP 269

Query: 225 ------------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENA 272
                       +G  A +         + G    P  +FL L+G++TL LRM   C+N 
Sbjct: 270 DVSYHGVVYTEALGPAAFIGRARVVPLRNTGAALSPQSAFLILQGIETLALRMDRICDNT 329

Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKG----GFDAAKRF 327
           LALA++L++HP +E V Y GL  HP H L +RQ  G   GI+S  LK        A  RF
Sbjct: 330 LALAKYLQSHPKVEWVRYAGLPDHPDHALVQRQSGGKASGILSFGLKSTDADPRAAGARF 389

Query: 328 CEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRG 387
            +  +LFT   ++G  +SL  HPA  TH  +      + G+S+++VRLSVGIE + DLR 
Sbjct: 390 LDALQLFTRLVNIGDAKSLATHPASTTHRQLNPEELAKAGVSESMVRLSVGIEHIDDLRA 449

Query: 388 DLERAL 393
           DL +AL
Sbjct: 450 DLVQAL 455


Lambda     K      H
   0.320    0.134    0.391 

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: 552
Number of extensions: 21
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 397
Length of database: 458
Length adjustment: 32
Effective length of query: 365
Effective length of database: 426
Effective search space:   155490
Effective search space used:   155490
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 (21.8 bits)
S2: 51 (24.3 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