GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Azospirillum brasilense Sp245

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.-; EC 1.2.1.103 (characterized, see rationale)
to candidate AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:Q5JFW1
         (330 letters)



>FitnessBrowser__azobra:AZOBR_RS07795
          Length = 350

 Score =  230 bits (586), Expect = 4e-65
 Identities = 147/349 (42%), Positives = 199/349 (57%), Gaps = 27/349 (7%)

Query: 2   IKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDL----RFT 57
           I+  ++GASGY G ELVR+L  HP VEI A+T+ R AG+ + +V P+L   +L    +  
Sbjct: 8   IRVGILGASGYTGAELVRMLLRHPGVEICALTAERQAGKPMAEVFPHLGQFNLPGLVKIE 67

Query: 58  NTKEFDADVIFLAVPHGTSMEIIDDYLGSAKIIDMSADFRLREDL-YREYYG-EHKRPEL 115
                  D +F A+PHGT+ E+I       K++D+SADFRL +   Y  +YG EH+  EL
Sbjct: 68  EVAWDKLDAVFCALPHGTTQEVIAGLPRHIKVVDLSADFRLSDPAEYATWYGHEHRAVEL 127

Query: 116 IEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFRELTDEAI------VDLKVSS 169
            +E  YGL E +R+ +RKA +VANPGC  T ++LAL P   L DE I      +D K   
Sbjct: 128 QKEVAYGLTEFNRQGVRKARVVANPGCYPTCSLLALLPL--LMDEMIEPGGIVIDAKSGV 185

Query: 170 SAGGRRENVASIHPERSHVVRVYKPYHHRHEGEVIQETGVKA------AFTVHSVDIIRG 223
           S  GR     ++  E S     Y   HHRH  E+ QE  + A      +FT H V + RG
Sbjct: 186 SGAGRDAKQQNLFTEVSEGFNAYGVGHHRHMPEIEQELRLAAGRPVTVSFTPHLVPMNRG 245

Query: 224 LLATIYFRF-EGSTRELLRKLLV--YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGF 280
           ++ATIY R  +G T + LR  L   Y+ EPFV +     G+   P  ++V  SN A IG 
Sbjct: 246 MMATIYVRMADGVTADDLRATLTARYESEPFVNVTA--AGIA--PATRHVRASNQALIGV 301

Query: 281 AHDEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329
             D     AI++S IDNL+KG SGQA+QNMN+MFGL E TGL   P++P
Sbjct: 302 FPDRTPRGAIIVSVIDNLVKGASGQAIQNMNVMFGLGETTGLEQAPLFP 350


Lambda     K      H
   0.321    0.140    0.404 

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: 292
Number of extensions: 16
Number of successful extensions: 6
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: 330
Length of database: 350
Length adjustment: 28
Effective length of query: 302
Effective length of database: 322
Effective search space:    97244
Effective search space used:    97244
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