GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Shewanella halifaxensis HAW-EB4

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_012277579.1 SHAL_RS12975 citrate synthase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>NCBI__GCF_000019185.1:WP_012277579.1
          Length = 429

 Score =  192 bits (487), Expect = 2e-53
 Identities = 128/381 (33%), Positives = 197/381 (51%), Gaps = 30/381 (7%)

Query: 19  QTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRD 78
           ++A++ +      L +RGY +  LA ++ + ++ YLLLYGELP +A+ + +   ++    
Sbjct: 54  ESAITYIDGEQGVLLHRGYPIDQLAVESDYLDLCYLLLYGELPNKAEYENFVYTVKTHTM 113

Query: 79  LPQALKEVLERIPADAHPMDVMRTGCSFLGNLEP-EQDFSQQHDKTDRLLAAFP------ 131
           + + L         DAHPM ++   C   G L    QD    +D+  R +AA+       
Sbjct: 114 VNEQLASFFRGFRRDAHPMAML---CGVTGALSAFYQDSLDVNDERHREIAAYRLVSKMP 170

Query: 132 --AIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVSLILY 184
             A MCY Y     GQ      +E+S  G+FL ++ G    E  V     + M+   IL+
Sbjct: 171 TIAAMCYKYSI---GQPFVYPRNELSYAGNFLSMMFGVPCEEYKVNPIVERAMDRIFILH 227

Query: 185 AEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIE 244
           A+HE NAST T R+  S+ ++ F+CI A I SL GP HGGANEA + M+E   S     E
Sbjct: 228 ADHEQNASTSTVRLAGSSGANPFACIAAGIASLWGPAHGGANEACLNMLEEIGSVDRIPE 287

Query: 245 GTLGMLARKD--KIMGFGHAIYKDNDPRNEVIKGWSKKLADE--VGDTVLFPVSE----A 296
                  ++D  ++MGFGH +YK+ DPR +V++    ++  E  V D +L    E    A
Sbjct: 288 FIARAKDKEDPFRLMGFGHRVYKNFDPRAKVMRETCHEVLAELKVNDPLLDVAMELERIA 347

Query: 297 IDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--QRANNRI 354
           ++   +  KKL+PN DFY       +GIPT +FT +F  +R  GW AH  E   +  ++I
Sbjct: 348 LEDEYFVSKKLYPNVDFYSGIIMKAIGIPTSMFTVLFALARTVGWIAHWKEMLDQPGHKI 407

Query: 355 IRPSAEYTGVEQRKFVPIEQR 375
            RP   YTG  +R F+  ++R
Sbjct: 408 SRPRQLYTGDPKRDFIDKDKR 428


Lambda     K      H
   0.321    0.135    0.406 

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: 358
Number of extensions: 23
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: 375
Length of database: 429
Length adjustment: 31
Effective length of query: 344
Effective length of database: 398
Effective search space:   136912
Effective search space used:   136912
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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