GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Echinicola vietnamensis KMM 6221, DSM 17526

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= BRENDA::Q5H4T8
         (397 letters)



>FitnessBrowser__Cola:Echvi_2080
          Length = 381

 Score =  416 bits (1069), Expect = e-121
 Identities = 205/380 (53%), Positives = 266/380 (70%), Gaps = 3/380 (0%)

Query: 15  LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVA 74
           +   T  IH G +PDP+TGA+M PI+ TSTY Q SPG+H+GFEYSRTHNPTR A ++ +A
Sbjct: 1   MKFGTKVIHAGVAPDPTTGAIMTPIFQTSTYVQKSPGQHKGFEYSRTHNPTRDALQKSIA 60

Query: 75  ALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFV 134
           ALE G     F+SGM A   +++LL  G  V++ +DLYGGT+R+F +V  +  G+ F FV
Sbjct: 61  ALENGKHGLCFSSGMGAIDALIKLLSPGDEVISTNDLYGGTYRIFTKVFAK-YGIKFHFV 119

Query: 135 DLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQ 194
            + DPA+ +  I   T+++W ETPTNPM+ ++DI A+A IA KH LL  VDNTFA+P LQ
Sbjct: 120 SMDDPASIEKYINDKTRLIWAETPTNPMMNIIDIKALAAIAGKHDLLLGVDNTFATPYLQ 179

Query: 195 RPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLA 254
            PL LGADLV+HS TKYL GHSD+V G  VV D+  LAE +AF+QNS G   GP D FL 
Sbjct: 180 NPLDLGADLVMHSVTKYLAGHSDVVMGALVVNDD-RLAEDLAFIQNSCGATPGPQDCFLV 238

Query: 255 LRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVS 314
           LRG+KTL LRM  HC+N   +A +L  HP ++KV +PG   HP H +A +QM  FGG++S
Sbjct: 239 LRGIKTLHLRMERHCQNGKTIAGYLRHHPKVDKVYWPGFEDHPNHDIAAKQMRDFGGMIS 298

Query: 315 IVLKGG-FDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALV 373
             + G   + AK+  E    F+LAESLGGVESL  HPA MTHASIP   RE++G++D+L+
Sbjct: 299 FSIVGDKQEDAKKVLENLHYFSLAESLGGVESLCGHPASMTHASIPKVEREKVGLTDSLI 358

Query: 374 RLSVGIEDLGDLRGDLERAL 393
           RLSVG+ED  DL+ DL  AL
Sbjct: 359 RLSVGVEDAEDLKNDLAAAL 378


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: 467
Number of extensions: 21
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: 397
Length of database: 381
Length adjustment: 30
Effective length of query: 367
Effective length of database: 351
Effective search space:   128817
Effective search space used:   128817
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