GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Klebsiella michiganensis M5al

Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate BWI76_RS12790 BWI76_RS12790 lactate dehydrogenase

Query= CharProtDB::CH_091799
         (329 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS12790 BWI76_RS12790 lactate
           dehydrogenase
          Length = 329

 Score =  595 bits (1534), Expect = e-175
 Identities = 295/329 (89%), Positives = 313/329 (95%)

Query: 1   MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60
           MK+AVYSTKQYDKKYLQ VN+++GFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV
Sbjct: 1   MKIAVYSTKQYDKKYLQHVNDAYGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60

Query: 61  LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120
           LEELK HGVKYIALRCAGFNNVDLDAAKELGL+VVRVPAY PEAVAEHAIGMMM+LNRRI
Sbjct: 61  LEELKAHGVKYIALRCAGFNNVDLDAAKELGLRVVRVPAYSPEAVAEHAIGMMMSLNRRI 120

Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSAA 180
           HRAYQRTRDANFSLEGLTGFTM+GKTAGVIGTGKIGVA LRILKGFGMRLLAFDPYPSAA
Sbjct: 121 HRAYQRTRDANFSLEGLTGFTMHGKTAGVIGTGKIGVAALRILKGFGMRLLAFDPYPSAA 180

Query: 181 ALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSRGALIDS 240
           AL++GVEYVDL TL+ ESDVISLHCPLT ENYHLLN AAFE+MK+GVMI+NTSRGALIDS
Sbjct: 181 ALDMGVEYVDLETLYRESDVISLHCPLTDENYHLLNHAAFERMKDGVMIINTSRGALIDS 240

Query: 241 QAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLT 300
           QAAI+ALK+QKIG+LGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLT
Sbjct: 241 QAAIDALKHQKIGALGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLT 300

Query: 301 AEALTSISQTTLQNLSNLEKGETCPNELV 329
           AEAL SISQTTL NL  +  G+ CPN LV
Sbjct: 301 AEALISISQTTLDNLRQVAAGDACPNALV 329


Lambda     K      H
   0.320    0.136    0.388 

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: 432
Number of extensions: 6
Number of successful extensions: 1
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: 329
Length of database: 329
Length adjustment: 28
Effective length of query: 301
Effective length of database: 301
Effective search space:    90601
Effective search space used:    90601
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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