GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Pseudomonas stutzeri RCH2

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF1148 Psest_1181 glyoxylate carboligase

Query= BRENDA::P9WG41
         (618 letters)



>FitnessBrowser__psRCH2:GFF1148
          Length = 593

 Score =  323 bits (829), Expect = 1e-92
 Identities = 203/587 (34%), Positives = 293/587 (49%), Gaps = 21/587 (3%)

Query: 35  LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94
           + ++    A +  L + G+D  FGIPG A+ P+Y  L     +RH+L RH +GA H A G
Sbjct: 1   MARMRAIDAAVAVLRKEGIDTAFGIPGAAINPLYSALRADGSIRHILARHVEGASHMAEG 60

Query: 95  YAHV-TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153
           Y     G +GVC+ TSGP  T+++T L  A  DSIP++ ITGQ  R  +  + FQ  DI 
Sbjct: 61  YTRTKAGNIGVCIGTSGPAGTDMITGLYSAWADSIPILCITGQAPRARLYKEDFQAVDIE 120

Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213
            I  P+TK    VR    +PRV  +AFH+  SGRPG VL+D+P DV   +  F       
Sbjct: 121 SIAKPVTKWAVTVREPALVPRVFQQAFHVMRSGRPGPVLIDLPFDVQMAEIEFDIETYEP 180

Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273
           L  YKP      +Q+ +A  ++ AA +P++  GGG+    A   L E AE  G+PV+ TL
Sbjct: 181 LAVYKPAAT--RKQIEKAIDMLCAAERPLIVAGGGIYNAGAEALLVEFAETVGVPVIPTL 238

Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332
           M  G+ PD H    GM G+  +     A +  SD ++ +G R+ +R TG ++ +  +   
Sbjct: 239 MGWGSIPDDHPLMAGMCGLQTSHRYGNANMLASDFVLGIGNRWANRHTGSVEVYTKDRTF 298

Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392
           +H DI+P +IG+    D  I  D  A +   + + +     G +     WA     RK  
Sbjct: 299 VHVDIEPTQIGRVFSPDFGITSDAGAALALFVEVAKERKAAGQLPDRTPWAADCQERKRT 358

Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452
            L         + P+ V + +    G DA +V+ +G  Q+ AAQF+   KPR W+N G  
Sbjct: 359 MLRKTHFDSVPMKPQRVYQCMNNAFGKDACYVSTIGLSQIAAAQFLHVYKPRHWINCGQA 418

Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512
           G +G+ IPAA+G   A P  +V A+ GD  FQ   +ELA  A   +P    L+NN  LG+
Sbjct: 419 GPLGWTIPAALGVVAADPTRKVVALSGDYDFQFMIEELAVGAQFKLPYIHILVNNAYLGL 478

Query: 513 VRQWQSLFYAERYSQ-------TDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVIN 565
           +RQ Q  F  +   Q        D +       D V + E LGC  +R  R+ED+   I 
Sbjct: 479 IRQSQRGFEMDYCVQLGFENINADQSGMEGYGVDHVAVVEGLGCKAIRVFRQEDLRPAIE 538

Query: 566 QAR---AINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPL 609
           QA+   A    PVVI+ I+         +A GT   EI A     PL
Sbjct: 539 QAQAWMAEYRVPVVIEVILERVTN----IAMGT---EIDAINEFEPL 578


Lambda     K      H
   0.319    0.136    0.414 

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: 958
Number of extensions: 59
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: 618
Length of database: 593
Length adjustment: 37
Effective length of query: 581
Effective length of database: 556
Effective search space:   323036
Effective search space used:   323036
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: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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