GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Thiomicrorhabdus arctica DSM 13458

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_019555914.1 F612_RS0101190 O-succinylhomoserine sulfhydrylase

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>NCBI__GCF_000381085.1:WP_019555914.1
          Length = 392

 Score =  347 bits (891), Expect = e-100
 Identities = 171/381 (44%), Positives = 252/381 (66%), Gaps = 2/381 (0%)

Query: 19  TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78
           T A+R G  +++  E SEA+F TS + Y  A  AAARFSG+++G  YSR  NPTV   E 
Sbjct: 8   TLAVRAGYDQTQEQENSEAIFPTSSFRYTSAAQAAARFSGEEKGNVYSRFTNPTVRAFEN 67

Query: 79  RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138
           R+AL+EG EAC  T+SGMAA+ +  +    +GDH+I  ++ FG+ + L +  L KFG+E 
Sbjct: 68  RLALMEGGEACVGTSSGMAAILSTFMALYESGDHVICSQSVFGTTKVLFNKYLVKFGLEV 127

Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198
           T V   D  ++  AI+PNTK FF ETP+NP  ++ DL  + A+A+  G + +VDN F TP
Sbjct: 128 TFVSQTDTSEWKKAIQPNTKAFFLETPSNPLTEIADLSTISALAKANGCLLIVDNCFCTP 187

Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258
            LQRP++ GAD++ +SATK +DGQGR + GAV G+ E ++  +  F R  GP++SPFNAW
Sbjct: 188 ILQRPLEQGADIIIHSATKFLDGQGRGIGGAVVGSNELVDEHVRGFMRTAGPSMSPFNAW 247

Query: 259 VVLKGLETLDLRIQRQSENALKVARF--LEGRVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316
           + LKGLETL +R+    ++AL++A +  L   V +V +PGL SHPQ+ LA  Q +A G +
Sbjct: 248 IFLKGLETLPIRMAAHCQSALQLAEWLSLHPAVEQVFYPGLKSHPQYELACKQQSAGGGL 307

Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376
            S ++ G + +A  ++D   ++ I+ N+GD ++ +THPA+TTH  V  D RL  G+ + +
Sbjct: 308 VSFKVKGNQAEAWSVIDHTQMVSITANLGDVKTSITHPATTTHVRVEPDARLRAGITDNL 367

Query: 377 LRLNVGLEDPEDLIADLDQAL 397
           +RL+VGLE  ED+ ADL + L
Sbjct: 368 IRLSVGLESIEDIKADLARGL 388


Lambda     K      H
   0.319    0.134    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: 377
Number of extensions: 9
Number of successful extensions: 2
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: 402
Length of database: 392
Length adjustment: 31
Effective length of query: 371
Effective length of database: 361
Effective search space:   133931
Effective search space used:   133931
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