GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Pseudomonas fluorescens FW300-N1B4

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate Pf1N1B4_5858 carboxyphosphonoenolpyruvate phosphonomutase, putative

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5858
          Length = 289

 Score =  125 bits (315), Expect = 9e-34
 Identities = 95/268 (35%), Positives = 142/268 (52%), Gaps = 12/268 (4%)

Query: 17  RELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGA-AITGSLAMPDLGLITLSELAMF 75
           R+L           V++P  A +A  +GFE   L G+ A    L  PD  LITLSE A  
Sbjct: 14  RQLFASNACYHTASVFDPMSARIAADLGFEVGILGGSVASLQVLGAPDFALITLSEFAEQ 73

Query: 76  TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKAL 135
            + I RV ++PVI DAD G+G A+NV RT+ ELERAG AA+ IED ++P + G  +   L
Sbjct: 74  ATRIGRVAQLPVIADADHGYGNALNVMRTIVELERAGVAALTIEDTLLPAQFGR-KSTDL 132

Query: 136 ISPEDMVKKIIAAVGARRDA--LIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALT 193
           I+  + V KI AA+ AR D+   I+ART+A G+   ++ + R + Y +AGAD I    + 
Sbjct: 133 ITVAEGVGKIRAALEARVDSEMAIIARTNA-GILPVQEIISRTKQYQQAGADGICMVGVR 191

Query: 194 SLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVL 253
             +   + A  +  PL+  +  +G       ++  E G ++ I     + A++KA+   L
Sbjct: 192 DFDHLEQIAEHLSVPLM--LVTYGNPLLRDDNRLAELGVRVTIDGHGAYFAAIKATYDSL 249

Query: 254 REIMEKGTQ-KDI----LDKLYTRTEFY 276
           RE  +  TQ  D+    L   YT+ E Y
Sbjct: 250 REQRQIFTQASDLSATELTHTYTQPEEY 277


Lambda     K      H
   0.321    0.137    0.378 

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: 188
Number of extensions: 12
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: 308
Length of database: 289
Length adjustment: 27
Effective length of query: 281
Effective length of database: 262
Effective search space:    73622
Effective search space used:    73622
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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