GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Pseudomonas putida KT2440

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate PP_4297 PP_4297 glyoxylate carboligase

Query= BRENDA::P9WG41
         (618 letters)



>FitnessBrowser__Putida:PP_4297
          Length = 591

 Score =  326 bits (835), Expect = 2e-93
 Identities = 194/560 (34%), Positives = 291/560 (51%), Gaps = 18/560 (3%)

Query: 35  LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94
           + ++    A +  +   GVD  FGIPG A+ P+Y  L     + HVL RH +GA H A G
Sbjct: 1   MSKMRAIDAAVLVMRREGVDTAFGIPGAAINPLYSALKKVGGIDHVLARHVEGASHMAEG 60

Query: 95  YAHVT-GRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153
           Y     G +GVC+ TSGP  T++VT L  A  DSIP++ ITGQ  R  +  + FQ  DI+
Sbjct: 61  YTRANPGNIGVCIGTSGPAGTDMVTGLYSASADSIPILCITGQAPRARLHKEDFQAVDIT 120

Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213
            I  P+TK    V     +P    +AF+   +GRPG VL+D+P DV   +  F       
Sbjct: 121 NIVKPVTKWATTVLEPGQVPYAFQKAFYEMRTGRPGPVLIDLPFDVQMAEIEFDIDAYEP 180

Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273
           LP +KP+      Q  +A  L+  A +P+L  GGG+I  +A+++L E AELTG+PV+ TL
Sbjct: 181 LPVHKPSAT--RVQAEKALALLNDAERPLLVAGGGIINADASDKLVEFAELTGVPVIPTL 238

Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332
           M  G  PD H Q +GM G+  +     A L +SDL+  +G R+ +R TG +D +    K 
Sbjct: 239 MGWGTIPDDHAQMVGMVGLQTSHRYGNATLLKSDLVFGIGNRWANRHTGSVDVYTEGRKF 298

Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392
           +H DI+P +IG+    D+ IV D    +   + + R     G ++    W      RK+ 
Sbjct: 299 VHVDIEPTQIGRVFTPDLGIVSDAGKALDVFLEVAREWKAAGKLKCRKAWLEECQERKSS 358

Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452
                   +  + P+ V E++ ++ G D  +V+ +G  Q+  AQF+   KPR W+N G  
Sbjct: 359 LQRKTHFDNVPVKPQRVYEEMNQVFGKDTCYVSTIGLSQIAGAQFLHVYKPRHWINCGQA 418

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

Query: 513 VRQWQSLF--------YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVI 564
           +RQ Q  F          E  + TD AT+     D V + E LGC  +R     ++   +
Sbjct: 479 IRQAQRGFDMDYCVQLAFENINSTDAATYG---VDHVAVVEGLGCKAIRVFEPAEIAPAL 535

Query: 565 NQARAIND---CPVVIDFIV 581
            +A+ + +    PVV++ I+
Sbjct: 536 IKAQKMAEEFRVPVVVEVIL 555


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: 54
Number of successful extensions: 5
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: 591
Length adjustment: 37
Effective length of query: 581
Effective length of database: 554
Effective search space:   321874
Effective search space used:   321874
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.

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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