GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Azorhizobium caulinodans ORS 571

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_043880593.1 AZC_RS21220 glutamate-5-semialdehyde dehydrogenase

Query= metacyc::AT2G39800-MONOMER
         (717 letters)



>NCBI__GCF_000010525.1:WP_043880593.1
          Length = 437

 Score =  265 bits (678), Expect = 3e-75
 Identities = 151/408 (37%), Positives = 233/408 (57%), Gaps = 8/408 (1%)

Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357
           M  AAR ++R L    +E +   L   A  + A    I A N  D+A A+  G+  +   
Sbjct: 28  MGRAARAAARTLALAPAEQKTAALKAAAARIRAATPEILAANADDMARARADGMSGAFQD 87

Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417
           RL +T  +I ++AA V  +A + DP+G V +     +GLV+E+  +PLGV+ +++ESRP+
Sbjct: 88  RLALTESRIEAIAAGVEMVAGLPDPVGAVTESWTRPNGLVIERVRTPLGVIGVIYESRPN 147

Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474
                A+L +R+GN ++L+GG ++  S+  +HK     + +  +    +  V  + R  +
Sbjct: 148 VTADAAALCVRAGNAVILRGGSDSLGSSGAIHKAFVAGLVDAGLSADCVQFVPFSDRTAV 207

Query: 475 PDLLK-LDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533
             +L  LD  +D+++PRG   LV ++++  ++PV  H DGI HVYV  A D DMAK ++ 
Sbjct: 208 GLMLGGLDGNLDVIVPRGGKGLVARVQSEARVPVFAHLDGIVHVYVHAAADLDMAKTVLL 267

Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKI---LNIPEA 590
           +AK+     C A ETLLV + +  +  L  L+  L   G  + G   A  +   +     
Sbjct: 268 NAKMRRTGICGAAETLLVDEKVAASQ-LKPLVEMLLDAGCEVRGDAAAQAVDPRVKPAVD 326

Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650
             ++ EY     +V++V D+  AIDHI  HGS HTD I+T D   A  FLR+VDSA V H
Sbjct: 327 ADWDTEYEDAIISVKLVPDLAAAIDHIETHGSHHTDSIITRDEAAAARFLREVDSAIVMH 386

Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698
           NAST+F+DG  FG GAE+G++TGR+HARGPVG E L + ++ + G GQ
Sbjct: 387 NASTQFADGGEFGFGAEIGIATGRMHARGPVGAEQLTSFKYRVHGNGQ 434


Lambda     K      H
   0.318    0.135    0.378 

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: 603
Number of extensions: 24
Number of successful extensions: 3
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: 717
Length of database: 437
Length adjustment: 36
Effective length of query: 681
Effective length of database: 401
Effective search space:   273081
Effective search space used:   273081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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