GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Salinicoccus carnicancri Crm

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_040608878.1 C792_RS0111230 glutamate-5-semialdehyde dehydrogenase

Query= BRENDA::Q941T1
         (735 letters)



>NCBI__GCF_000330705.1:WP_040608878.1
          Length = 423

 Score =  249 bits (635), Expect = 3e-70
 Identities = 140/414 (33%), Positives = 236/414 (57%), Gaps = 7/414 (1%)

Query: 311 EATAREMAVAARDCSRHLQKLSSEERKKILLDIADALEANEDLITSENQADLDLAQDIGY 370
           EA    +   A+  ++ L+KLS++E+   L  +   LE +   I   N  D++  +  G 
Sbjct: 9   EAIIENLGTKAKHAAKVLRKLSAKEKDAALEAMIGGLENHAGKILEANSKDIENGKKNGL 68

Query: 371 DKSLVARMTIKPGKIKSLAGSIREIADMEDPISHTLKRTEVAKDLVFEKTYCPLGVLLII 430
             +LV R+T+   ++  +   +R++ ++ DP +    +    + L   K   PLGV+ II
Sbjct: 69  GDALVERLTLNEERLAGMQDGLRQMTELTDPTTQNEGQWINEQGLKIGKVRVPLGVIGII 128

Query: 431 FESRPDALVQIASLAIRSGNGLLLKGGKEAMRSN-TILHKVITGAIPDVVGKKLIGLVKN 489
           +ESRP+  V  + L +++GN ++L+GGKEAM SN  I+  +  G     V K+ + L+ +
Sbjct: 129 YESRPNVTVDASGLCLKAGNAVILRGGKEAMNSNRAIVEALQEGLSGTAVPKESVQLITD 188

Query: 490 --KDEIADLLKLDDVIDLVIPRGSNKLVSQIKAATKIPVLGHADGICHVYIDKSADMDMA 547
             ++  A+ ++ ++ +D +IPRG   L+  +     +PV+    G CH+YI +SAD +MA
Sbjct: 189 PSRELAAEFMQANEYVDCLIPRGGAGLIQTVLKQATVPVIETGTGNCHLYIHESADPEMA 248

Query: 548 KRIVLDAKVDYPAACNAMETLLVHKDLNRTEGLDDLLVELEKEGVVIYGGPVAHDTLK-- 605
           K ++++AK    + CNA+ETLL+   +   E L  L   L + GV I+G       +   
Sbjct: 249 KSLLINAKTHRVSVCNALETLLIDDSIAEKE-LPALGEALLEAGVAIHGDEKTCSLISEA 307

Query: 606 LPKVDS-FHHEYNSMACTLEFVDDVQSAIDHINRYGSAHTDCIITTDGKAAETFLQQVDS 664
           +P  ++ +  EY      ++ VD  ++AIDHI+ Y + H+D I  TD +  + FL +VDS
Sbjct: 308 VPATEADYSEEYLGYEIAVKVVDGYEAAIDHIDGYSTGHSDVIAATDYQTIQNFLNEVDS 367

Query: 665 AAVFHNASTRFCDGARFGLGAEVGISTGRIHARGPVGVDGLLTTRCILRGSGQV 718
           AAV+ NASTRF DG  FG G E+GIST ++HARGP+G++ L + + ++ GSGQ+
Sbjct: 368 AAVYANASTRFTDGEMFGFGGEIGISTQKLHARGPMGLEALTSYKYVVEGSGQI 421


Lambda     K      H
   0.318    0.136    0.385 

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: 668
Number of extensions: 29
Number of successful extensions: 3
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: 735
Length of database: 423
Length adjustment: 36
Effective length of query: 699
Effective length of database: 387
Effective search space:   270513
Effective search space used:   270513
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 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