GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Amycolatopsis halophila YIM 93223

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>NCBI__GCF_000504245.1:WP_034272173.1
          Length = 393

 Score =  302 bits (773), Expect = 1e-86
 Identities = 176/390 (45%), Positives = 231/390 (59%), Gaps = 24/390 (6%)

Query: 17  MVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWH 76
           M+ NY   A   VRG G+ V+D  G   +D  GGIAVN LGHAHPA+V A++EQ   L H
Sbjct: 11  MMDNYGTPALELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGH 70

Query: 77  VSNVFTNEPALRLAHKLVD-ATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIV 135
            SN++ N  AL LA  L+D A  + +V FCNSGAEA EAA K+ R        T K ++V
Sbjct: 71  TSNLYINPVALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-------TGKSKLV 123

Query: 136 AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPI 195
           A    FHGRT+  ++V GQ    + F P + G+THVP+ D AAL++AV   T AV +EP+
Sbjct: 124 ACDGGFHGRTMGALSVTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPV 183

Query: 196 QGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAK 255
            GEGGV+PA   +L+ ARE+  A  ALLV DEVQTG+GR G  FA+Q  GVTPD++T AK
Sbjct: 184 LGEGGVVPAPDGFLRAAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAK 243

Query: 256 SLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKH 315
            LGGG P+ A++      + L  G HGTT+GGNP+ACA   AVI  I    +L+ V    
Sbjct: 244 GLGGGLPLGAVIGIGQTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLG 303

Query: 316 DKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDV 375
                 + ++   + L +EVRG GLL G  L+   K  A  +  AA+R G +I    PDV
Sbjct: 304 KDLAAGVRKL--DHPLVSEVRGAGLLQGIGLT---KPVAPTVATAAQRAGYLINPVQPDV 358

Query: 376 IRFAPSLVVED-----------ADIDAGLD 394
           IR AP L++ +           A +D GLD
Sbjct: 359 IRLAPPLIITERQVADFLAALPAALDVGLD 388


Lambda     K      H
   0.320    0.136    0.400 

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: 447
Number of extensions: 26
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: 406
Length of database: 393
Length adjustment: 31
Effective length of query: 375
Effective length of database: 362
Effective search space:   135750
Effective search space used:   135750
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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