GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Klebsiella michiganensis M5al

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__Koxy:BWI76_RS26000
          Length = 406

 Score =  736 bits (1899), Expect = 0.0
 Identities = 357/406 (87%), Positives = 380/406 (93%)

Query: 1   MAIEQTAITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCH 60
           MA EQ AITRATFDEVILPIYAPAEFIPVKG+GSR+WDQQGKEYVDFAGGIAVTALGHCH
Sbjct: 1   MATEQPAITRATFDEVILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCH 60

Query: 61  PALVNALKTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLAR 120
           PALV AL  QGE LWH SNVFTNEPALRLGRKL++ATFA+RVVFMNSGTEANETAFKLAR
Sbjct: 61  PALVAALHEQGEKLWHTSNVFTNEPALRLGRKLVDATFADRVVFMNSGTEANETAFKLAR 120

Query: 121 HYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVK 180
           HY   RHSP+KTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADI+HVPFNDLHAVK
Sbjct: 121 HYTVTRHSPYKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVK 180

Query: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFA 240
           AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLR+LCDQHQALLVFDEVQCGMGRTG LFA
Sbjct: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFA 240

Query: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFD 300
           YMHYGVTPDILTSAKALGGGFPISAMLTT +IASAFH GSHGSTYGGNPLACAV GAAFD
Sbjct: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFD 300

Query: 301 IINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYA 360
           +INTPEVL+G+ AKR+ FV HLQ+ID ++D+FSDIRGMGLLIGAELKPQY G+ARDFLYA
Sbjct: 301 LINTPEVLDGVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYA 360

Query: 361 GAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406
            AEAGVMVLNAGPDVMRF PSLV++D+DI EGM RFA AV +V+ A
Sbjct: 361 AAEAGVMVLNAGPDVMRFVPSLVIDDSDIAEGMARFAQAVERVLSA 406


Lambda     K      H
   0.322    0.138    0.415 

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: 723
Number of extensions: 21
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 (21.9 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