GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Amycolatopsis halophila YIM 93223

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_051399596.1 AMYHA_RS06280 citrate synthase

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



>NCBI__GCF_000504245.1:WP_051399596.1
          Length = 438

 Score =  213 bits (543), Expect = 6e-60
 Identities = 129/379 (34%), Positives = 209/379 (55%), Gaps = 21/379 (5%)

Query: 17  AGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQL 76
           A  +A++ +      L YRGY +  LA  + F EV+YLL+YGELPT+ QL  + G++ + 
Sbjct: 61  ATSSAITYIDGDAGILRYRGYPIEQLAEHSNFIEVSYLLIYGELPTERQLADFNGRIERH 120

Query: 77  RDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQ----DFSQQHDKTDRLLAAFPA 132
             L + LK   +  P DAHPM V+ +  S L     +     D       T R+LA  P 
Sbjct: 121 TLLHEDLKRFFDGFPRDAHPMPVLSSAVSALSTFYQDSLNPFDEPSVELSTVRMLAKVPT 180

Query: 133 IMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHG--KKPSELH---VKVMNVSLILYAEH 187
           +  Y Y+ S  GQ      + +S+  +FL +  G   +P E+     K +++  IL+A+H
Sbjct: 181 LAAYAYKKS-IGQPFLYPDNSLSLVENFLRMTFGLPAEPYEIDPDIAKALDLLFILHADH 239

Query: 188 EFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTL 247
           E N ST T R+  S+ ++LF+ ++A I +L GPLHGGAN A ++M+E   +    ++  +
Sbjct: 240 EQNCSTSTVRLVGSSEANLFASVSAGINALFGPLHGGANAAVLDMLEDIRADGGDVDRFV 299

Query: 248 GMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDT-VLFPVSEAIDKT--- 300
             +  K+   ++MGFGH +YK+ DPR ++IK  + ++   +G +  L  +++ +++T   
Sbjct: 300 SRVKNKEAGVRLMGFGHRVYKNYDPRAKIIKKTADEILGRLGKSDELLDIAKKLEETALS 359

Query: 301 --MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRAN--NRIIR 356
              + ++KL+PN DFY    Y  +G PT+ FT +F   RL GW AH  E   +   +I R
Sbjct: 360 DDYFVERKLYPNVDFYTGLIYRALGFPTEYFTVLFALGRLPGWIAHWREMMLDPARKIGR 419

Query: 357 PSAEYTGVEQRKFVPIEQR 375
           P   YTG  +RK++ IE+R
Sbjct: 420 PRQVYTGAPERKYLDIEKR 438


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: 400
Number of extensions: 21
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: 438
Length adjustment: 31
Effective length of query: 344
Effective length of database: 407
Effective search space:   140008
Effective search space used:   140008
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