GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Sinorhizobium meliloti 1021

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase

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



>FitnessBrowser__Smeli:SMc02138
          Length = 399

 Score =  487 bits (1253), Expect = e-142
 Identities = 245/379 (64%), Positives = 290/379 (76%)

Query: 8   TYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSN 67
           TY RA + FERGEG +L A DG R+LDFAAGVAVN LGHA+P+LVEAL AQA K+WH SN
Sbjct: 10  TYLRAPLRFERGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLSN 69

Query: 68  LFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQ 127
           L+ +AGQESLA+RLT+ TFAD VFFTNSGAEA EC  K  R+YH+ KG   +  +ITFE 
Sbjct: 70  LYEIAGQESLARRLTQVTFADRVFFTNSGAEALECAIKTARRYHFAKGHVEKFHVITFEG 129

Query: 128 AFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEG 187
           AFHGRTLA ++A  Q+K I+GFGP   GF  VPFGD+ AV+NA+ +ETA I +EPIQGEG
Sbjct: 130 AFHGRTLATIAAGGQQKYIEGFGPKAPGFYQVPFGDIGAVKNAINEETAAILVEPIQGEG 189

Query: 188 GIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGG 247
           GIR  S EF++GLRE+CDE GLLL LDE+Q G+GRTGKLFAHEWAGI PD+MAVAKGIGG
Sbjct: 190 GIRTASKEFMQGLRELCDEFGLLLILDEVQSGVGRTGKLFAHEWAGIKPDIMAVAKGIGG 249

Query: 248 GFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQ 307
           GFPLGACLATE AA+GM AGTHGSTYGGNPLA AVGNAVLD VL  GFLD V+ +  + +
Sbjct: 250 GFPLGACLATEAAAAGMVAGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLDQVREVALVFR 309

Query: 308 DRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLPPL 367
             LA L    P V + +RG GLMLG+       D++ A+RA  LL VPAG+NV+RLLPPL
Sbjct: 310 QGLASLKDRFPDVIEEIRGDGLMLGIKAKVPSADLLKAIRAEKLLVVPAGENVLRLLPPL 369

Query: 368 NIGEAEVEEAVAILAKTAK 386
               AE  E +A L + A+
Sbjct: 370 ITTPAEAREGLARLERAAE 388


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: 514
Number of extensions: 16
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: 399
Length adjustment: 31
Effective length of query: 358
Effective length of database: 368
Effective search space:   131744
Effective search space used:   131744
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