GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate HSERO_RS11425 HSERO_RS11425 aconitate hydratase

Query= curated2:Q9WZ24
         (417 letters)



>FitnessBrowser__HerbieS:HSERO_RS11425
          Length = 873

 Score =  117 bits (292), Expect = 2e-30
 Identities = 110/343 (32%), Positives = 150/343 (43%), Gaps = 46/343 (13%)

Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173
           D +VG DSHT    ALG  A GVG  +     L    W R+P+ I V L G+ +  +TA 
Sbjct: 194 DTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGRRQPGITAT 253

Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233
           D+VL L   L         +EF G G   +++  R TISNMA E G    +F +D+ TI 
Sbjct: 254 DIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDRATISNMAPEYGATAAMFSIDQQTID 313

Query: 234 YERERGIEVEE------------MYPDEDAK--YVREVEMDLSELEPQVAYPFLPSNAKD 279
           Y +  G E E+            ++ D  AK  Y R +  DLS +   +A P  P     
Sbjct: 314 YLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYERVLRFDLSTVVRTLAGPSNPHKRLP 373

Query: 280 VSEAEKERI--KIDQ------------AVIGSCTNGRIEDLRLAAQILK------GRTVS 319
           VSE   + I  K++             A I SCTN       +AA +L       G    
Sbjct: 374 VSELAAQGIAGKVENEPGKMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANRLGLARK 433

Query: 320 PDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLG--GHMGVLAEGEV--- 374
           P V+  + PGS+ V     + GL       G  +    C  C G  G +    + E+   
Sbjct: 434 PWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTCNGMSGALDPKIQQEIIDR 493

Query: 375 -----AISTTNRNFVGRMGHPNSK-VFLASPAVAAASAIKGYI 411
                A+ + NRNF GR+ HP +K  FLASP +  A AI G I
Sbjct: 494 DLYSTAVLSGNRNFDGRI-HPYAKQAFLASPPLVVAYAIAGTI 535


Lambda     K      H
   0.318    0.138    0.395 

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: 711
Number of extensions: 35
Number of successful extensions: 2
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: 417
Length of database: 873
Length adjustment: 37
Effective length of query: 380
Effective length of database: 836
Effective search space:   317680
Effective search space used:   317680
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 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