GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Phyllobacterium endophyticum PEPV15

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_106716014.1 CU100_RS04930 aspartate aminotransferase family protein

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>NCBI__GCF_003010935.1:WP_106716014.1
          Length = 401

 Score =  470 bits (1210), Expect = e-137
 Identities = 234/381 (61%), Positives = 285/381 (74%)

Query: 8   TYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSN 67
           TYARAD+ FERGEG +L+   G R+LDFAAG+AVN LG+++P+LV AL AQA KLWH SN
Sbjct: 12  TYARADLRFERGEGVWLFTDSGIRYLDFAAGIAVNSLGYSHPHLVTALKAQADKLWHLSN 71

Query: 68  LFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQ 127
           ++ + GQE L +RL + TFAD VFFTNSGAEA EC  K  R+YHY  G+  R RIITFE 
Sbjct: 72  IYEIPGQERLGQRLVDNTFADKVFFTNSGAEALECAIKTARRYHYVNGEHERFRIITFEG 131

Query: 128 AFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEG 187
           AFHGRTLA ++A  Q K ++GFGP ++GFD VPFGD+ A++ A+  ETA I +EP+QGEG
Sbjct: 132 AFHGRTLATIAAGGQPKYLEGFGPKVEGFDQVPFGDVNALKAAIGPETAAILIEPVQGEG 191

Query: 188 GIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGG 247
           G+R    E LR LR +CDEHGLLL LDE+Q GMGRTGKLFAHEW+GI PD+MAVAKGIGG
Sbjct: 192 GVRPVPEEELRALRGLCDEHGLLLILDEVQTGMGRTGKLFAHEWSGIQPDIMAVAKGIGG 251

Query: 248 GFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQ 307
           GFPLGACLAT +AA GMTAG HG+TYGGNPLA AVGNAVLD +LE GFL+ VQ +  +++
Sbjct: 252 GFPLGACLATAEAAKGMTAGVHGTTYGGNPLAMAVGNAVLDVILEEGFLERVQHVALIMK 311

Query: 308 DRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLPPL 367
             LA +    P     VRG+G ++GL C      +V ALR   LL+V AGDNVVRLLPPL
Sbjct: 312 QGLASISDRYPEAISEVRGRGFLIGLKCRVPNTTMVQALRDEHLLTVGAGDNVVRLLPPL 371

Query: 368 NIGEAEVEEAVAILAKTAKEL 388
              EA+V EA+A +   A+ L
Sbjct: 372 VATEADVREALARIEAAAERL 392


Lambda     K      H
   0.321    0.139    0.414 

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: 496
Number of extensions: 18
Number of successful extensions: 1
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: 389
Length of database: 401
Length adjustment: 31
Effective length of query: 358
Effective length of database: 370
Effective search space:   132460
Effective search space used:   132460
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 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