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_34 Methionine gamma-lyase (EC 4.4.1.11)

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_34
          Length = 434

 Score =  310 bits (795), Expect = 4e-89
 Identities = 176/399 (44%), Positives = 242/399 (60%), Gaps = 13/399 (3%)

Query: 6   THSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYA--------QSSPGEHQGFE 57
           T + D   A   +T AIH G +P    GA++PPI+ ++TYA        +   G+  G+ 
Sbjct: 2   TRTTDRSPATGFSTRAIHHGYNPADHQGALVPPIHTSATYAFPDVAYGARCFAGQEPGYF 61

Query: 58  YSRTHNPTRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTF 116
           Y+R  NPT    E  +AALE G  A  F SGM A T+T+  +L+ G  ++A   LYG TF
Sbjct: 62  YTRIANPTLALLEGRLAALEEGAGAVVFGSGMGAITATLWSMLEPGDEILADLTLYGCTF 121

Query: 117 RLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIAR 176
                   R  G+    VD+TDPA    A+ A T+++++ETP NP ++LVDIAA++ +A 
Sbjct: 122 SFLHHGLGRF-GVTVRHVDMTDPARVAEALTAKTRVLYLETPANPNMRLVDIAAVSALAH 180

Query: 177 KHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMA 236
             G   VVDNT+ +P LQ+PL LGAD+ VHS TKYL GH D+  G AV  D AELA+++ 
Sbjct: 181 AQGAKVVVDNTYCTPYLQQPLLLGADVSVHSMTKYLGGHGDLTAGAAVFAD-AELAQRVR 239

Query: 237 F--LQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLA 294
              L++  G V    D+ L +RGLKTL LRM  HC++A  +A+++  HPA   V YPGL 
Sbjct: 240 LYGLKDMTGAVMSAQDAHLVMRGLKTLALRMDRHCQSAQKVAEFIAAHPAAAAVHYPGLP 299

Query: 295 SHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMT 354
           S  QH LAK+QM   GG+++  L+GG  A  RF +  +L T A SLG  E+L  HPA MT
Sbjct: 300 SFAQHALAKQQMRQMGGMIAFELRGGLQAGVRFMDALQLVTRAVSLGDAETLAQHPASMT 359

Query: 355 HASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
           H++    +R   GI++ LVRLSVG+EDL DL  D+ +AL
Sbjct: 360 HSTYTPEQRAAHGIAEGLVRLSVGLEDLDDLLADIGQAL 398


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: 497
Number of extensions: 24
Number of successful extensions: 5
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: 397
Length of database: 434
Length adjustment: 31
Effective length of query: 366
Effective length of database: 403
Effective search space:   147498
Effective search space used:   147498
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: 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