GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Desulfovibrio vulgaris Miyazaki F

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate 8500980 DvMF_1717 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= curated2:A0RWW0
         (348 letters)



>FitnessBrowser__Miya:8500980
          Length = 350

 Score =  267 bits (682), Expect = 3e-76
 Identities = 144/351 (41%), Positives = 207/351 (58%), Gaps = 8/351 (2%)

Query: 1   MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFT--DLTFSE 58
           ++ G+VG +GY G E  RLL  HP++ +   TSR   G  L  + P LRG    +   + 
Sbjct: 4   IRAGLVGVTGYTGMELTRLLAGHPNMRLVRATSRTEAGRPLSDIYPFLRGLPGGNAVMTA 63

Query: 59  LDYDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHP 118
            D D L+D+CD+ F AVPHG A ++   L  R ++V+DLSAD+RL DP  Y  WY   H 
Sbjct: 64  PDPDDLADNCDVAFLAVPHGAAMEMGATLRQRGLRVVDLSADFRLRDPDVYEAWYKVPHT 123

Query: 119 HPDYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKI 178
               L ++V+G+PEL+ + ++ A LV+ PGC    +IL L   ++ GLV+T+ IVVD+K 
Sbjct: 124 RRAELPQAVYGLPELYGDAVKKAGLVANPGCYPTATILGLYAALKHGLVETDGIVVDAKS 183

Query: 179 GSSGAG--AGAGTAHAMRAGVIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVV 236
           G++GAG  A  GT     +   R Y   KHRHT EIEQELS IAG  + VS +PH + + 
Sbjct: 184 GATGAGRKAAVGTLFCEVSDTFRAYNIGKHRHTPEIEQELSAIAGTSMVVSFNPHLLPIN 243

Query: 237 RGILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDI 296
           RGIL T +  L +  S +D+   + Q +   R+VR++       + P+ + + G+ FCD+
Sbjct: 244 RGILATIYAKLAKPVSPQDVQAAFEQTWQGSRWVRVL----PAGQLPETRHVRGTMFCDV 299

Query: 297 GFDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347
           G   D+  NRLV +SA DNL +GA+G A+ N N+M GL   +GL   PL P
Sbjct: 300 GVVTDQRTNRLVILSAIDNLCRGASGQAVANANLMFGLPVETGLMLAPLMP 350


Lambda     K      H
   0.320    0.137    0.412 

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: 291
Number of extensions: 14
Number of successful extensions: 4
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: 348
Length of database: 350
Length adjustment: 29
Effective length of query: 319
Effective length of database: 321
Effective search space:   102399
Effective search space used:   102399
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: 49 (23.5 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