GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Caldicellulosiruptor kronotskyensis 2002

Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_013430065.1 CALKRO_RS05450 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::O04226
         (716 letters)



>NCBI__GCF_000166775.1:WP_013430065.1
          Length = 419

 Score =  270 bits (689), Expect = 1e-76
 Identities = 149/413 (36%), Positives = 241/413 (58%), Gaps = 11/413 (2%)

Query: 297 EMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLV 356
           E A   ++ S+ + N+S  E+ + L  ++  +    D I  EN+ D+  A   G +  L+
Sbjct: 6   EKAKKVKEASKKIMNISENEKNRALSCISQKILEKMDFILQENQKDMENAVSKGIKGALL 65

Query: 357 ARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRP 416
            RL +   +I  + K I  +  + DP+ +++   +  + L++ +   P+G + I++E+RP
Sbjct: 66  DRLKLTEDRIKQICKGIEDVIKLPDPVGEVISMWKRPNGLLIGQKRVPIGAIGIIYEARP 125

Query: 417 DALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDA-IPRNVGEKLIGLV--TTRDE 473
           +  V  A L +++GN +LL+GG EAI SN  L KV+ +  I   + E  I +V  T+R+ 
Sbjct: 126 NVTVDAAVLCLKAGNSVLLRGGSEAINSNIALVKVMKEGLIEAGIEESSIEIVEDTSRET 185

Query: 474 IADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVM 533
              ++KL++ +DL+IPRG   L+  +  +  +PV+    G CHV++D+SAD +MAK IV+
Sbjct: 186 AVAMMKLNEYLDLLIPRGGANLIKTVVQNATVPVIETGVGNCHVFVDESADFEMAKEIVI 245

Query: 534 DAKIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKA-------LG 586
           +AK   P  CNA E LLVH+++ +   L  IL  L    V I G  +  +        + 
Sbjct: 246 NAKTQRPGVCNAAEKLLVHRNIAEE-FLPMILKELMERNVEIRGCSLTAEICRKNGIEIK 304

Query: 587 FPKAVSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSA 646
                 ++ EY  +   V+ VD +  AI+HI++YGS H++ IVT D   A+ FL  VD+A
Sbjct: 305 LATEEDWYTEYLDLIMGVKVVDSIDDAIEHINKYGSKHSEAIVTKDYFNAQKFLDYVDAA 364

Query: 647 AVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699
           AV+ NASTRF+DG  FG GAE+GIST ++HARGP+G++ L T ++I+ G GQV
Sbjct: 365 AVYVNASTRFTDGFEFGFGAEIGISTQKLHARGPMGLKELTTIKYIIYGSGQV 417


Lambda     K      H
   0.317    0.134    0.377 

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: 604
Number of extensions: 19
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: 716
Length of database: 419
Length adjustment: 36
Effective length of query: 680
Effective length of database: 383
Effective search space:   260440
Effective search space used:   260440
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: 52 (24.6 bits)

This GapMind analysis is from Jul 26 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