GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Desulfotalea psychrophila LSv54

Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_011190179.1 DP_RS14870 pyridoxal phosphate-dependent aminotransferase

Query= curated2:O07587
         (393 letters)



>NCBI__GCF_000025945.1:WP_011190179.1
          Length = 395

 Score =  340 bits (871), Expect = 5e-98
 Identities = 172/389 (44%), Positives = 247/389 (63%), Gaps = 5/389 (1%)

Query: 6   LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEK 65
           +S +++    K SWIRK+F++G ++K EFG + VFDFSLGNP   PP  F + L + A  
Sbjct: 3   ISSKMKIFAEKSSWIRKMFEQGGKMKAEFGAENVFDFSLGNPDAPPPAQFDQVLAKIAAD 62

Query: 66  ---GSHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGE 122
              G+H Y+ N G L  RE VA  +         A  ++++ GA G +NV +KS++NPG+
Sbjct: 63  NGPGTHSYMPNGGHLWVREAVAGQMAKEQGVKVVASDMLLSCGAAGGINVIMKSLLNPGD 122

Query: 123 EVIILAPYFAEYKLYIENYGGKAVSCPLTSRFEIDIEAVRQSITPQTKGLILNTPHNPTG 182
           EVI LAPYF EY  Y++N+GGK+        F  D+ A+R++I+ +TK +I+N+P+NPTG
Sbjct: 123 EVIFLAPYFVEYDFYVDNHGGKSRVVQTDENFNPDMAAIREAISEKTKAIIINSPNNPTG 182

Query: 183 TVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYDE-ELANPFQSYHRVILASSF 241
            + S++ + +LG LL E+ EK G TIY++ DEPY ++ YD  E+ + F +Y   I+ SS+
Sbjct: 183 QIYSKEILAELGLLLTEMGEKFGSTIYLISDEPYRKITYDGIEVPSIFAAYSNSIIVSSY 242

Query: 242 SKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVDA 301
           SKDL + GER+GY+ +   + +   L++A    NR LGFVNAP +MQR +A +  + VD 
Sbjct: 243 SKDLSLPGERIGYVAVHPGISEKAELVSAMTLANRILGFVNAPALMQRVIAELQGISVDN 302

Query: 302 SAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSGF 361
             Y  RR+    IL EAGF+F  PKG F++FPKSPIED+VAFC    Q+ K+L VP  GF
Sbjct: 303 ERYARRREAFCQILTEAGFDFVPPKGAFYIFPKSPIEDDVAFCA-ILQEEKILAVPGRGF 361

Query: 362 GMSGHFRLSFSVPIEQIKNSRDIFISLYK 390
           G  G+ RL+F VP E I  S   F   Y+
Sbjct: 362 GAPGYIRLAFCVPDETIAGSAAAFKRAYQ 390


Lambda     K      H
   0.320    0.139    0.396 

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: 425
Number of extensions: 17
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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