GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Paraburkholderia bryophila 376MFSha3.1

Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate H281DRAFT_02928 H281DRAFT_02928 uncharacterized oxidoreductase

Query= curated2:Q07251
         (349 letters)



>FitnessBrowser__Burk376:H281DRAFT_02928
          Length = 367

 Score =  217 bits (553), Expect = 3e-61
 Identities = 123/312 (39%), Positives = 176/312 (56%), Gaps = 5/312 (1%)

Query: 26  ADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCVLDQGTLMVFDGDGGF 85
           A+ VA+HLV ++  G+ SHG+ ++P Y  +L    +     A  V D G ++  +G  GF
Sbjct: 37  AELVADHLVAANLTGHDSHGVGMIPRYVASLADGQLQLNLHADVVKDAGAVLTVEGRKGF 96

Query: 86  GQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAAGFVLLSFTNVINRAP 145
           GQ V    M+  I R ++ G C V LR +HH+GR+GH+ E  A AG V   F NV    P
Sbjct: 97  GQVVAFEAMEEGIARAQRIGICAVGLRDAHHIGRIGHWAEQCARAGLVSFHFVNVAG-DP 155

Query: 146 VVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAINKARVLAEKGEPAPEGSII 205
           +VAPFGG   R+ TNP C A P P G+PPLV+D ATS +A  K RV   +G+  P G++I
Sbjct: 156 LVAPFGGADRRIGTNPFCAAYPRP-GKPPLVLDFATSTVAYGKTRVAYNQGKQVPPGALI 214

Query: 206 GADGNPTTDASTMFGEHPGALLPFGGHKGYALGVVAELLAGVLSGGGTIQPDN-PRGGVA 264
             +G PT D   M  E  G+L PFGGHKG+ L  + E+ +G L+GG T   D        
Sbjct: 215 DHEGVPTADPKVMHEEPFGSLTPFGGHKGFGLAAMCEIFSGALAGGFTTHADTLGTTNAI 274

Query: 265 TNNLFAVLLNPALDLGLDWQSAEVEAFVRYLHDTPPAPGVDRVQYPGEYEAANRAQ-ASD 323
            N + +V+++PA     D Q AE +AF+ ++  +P A GVD +  PGE E   RA+  + 
Sbjct: 275 INCMLSVIIDPAAFDAPDAQ-AEADAFIAWVKASPLAAGVDHIYEPGEPERVTRAEREAQ 333

Query: 324 TLNINPAIWRNL 335
            + ++ A W  +
Sbjct: 334 GIPVDAATWTQI 345


Lambda     K      H
   0.319    0.136    0.409 

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: 343
Number of extensions: 20
Number of successful extensions: 4
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: 349
Length of database: 367
Length adjustment: 29
Effective length of query: 320
Effective length of database: 338
Effective search space:   108160
Effective search space used:   108160
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 (21.7 bits)
S2: 49 (23.5 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