GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Sinorhizobium meliloti 1021

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate SM_b20262 SM_b20262 semialdehyde dehydrogenase

Query= SwissProt::Q08IC0
         (525 letters)



>lcl|FitnessBrowser__Smeli:SM_b20262 SM_b20262 semialdehyde
           dehydrogenase
          Length = 505

 Score =  499 bits (1285), Expect = e-146
 Identities = 270/502 (53%), Positives = 331/502 (65%), Gaps = 7/502 (1%)

Query: 5   GEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQPL 64
           G+ L+  E + G AGT  A  P+ G   D   F V     V RACE A +AF  Y     
Sbjct: 7   GKHLVAGEWLDG-AGTF-ASAPAHGPAHD---FAVGTVELVNRACEAAEEAFWTYGYSSR 61

Query: 65  AARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGRFL 124
             RAAFL AIADEI A  +A+ E    ETGLP ARL GERGRT GQLRLFA  +  G +L
Sbjct: 62  KERAAFLRAIADEIEARAEAITEIGSQETGLPEARLNGERGRTTGQLRLFADHIEKGDYL 121

Query: 125 AASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPVIV 184
              +D A P R P PR ++RL +  +GPV VFGASNFPLAFS AGGDTA+ALAAGCPV+V
Sbjct: 122 DRRVDAAMPERQPAPRQEIRLVQRPVGPVAVFGASNFPLAFSTAGGDTAAALAAGCPVVV 181

Query: 185 KAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTGSR 244
           K H AH GT E+V  A+ AA+ KTG+  GVFSL+ G  R +G ALV HP ++AVGFTGS 
Sbjct: 182 KGHSAHPGTGEIVAEAVDAAIRKTGVHPGVFSLIQGGSRDVGHALVQHPHIKAVGFTGSL 241

Query: 245 QGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQFCT 304
            GG AL  +  ARP+PIP + E+ S+NP+ L P AL AR + +  G+  SLT+G GQFCT
Sbjct: 242 AGGRALFDLCAARPEPIPFFGELGSVNPMFLLPEALKARAETLGQGWAGSLTMGAGQFCT 301

Query: 305 NPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIGAG 364
           NPG+ + I+G D DRF T A +ALAK     MLT GIA AYR+G+ + A    V+ + A 
Sbjct: 302 NPGIAVVIEGADADRFTTAAVEALAKVAPQTMLTDGIAKAYRDGQARFATRNAVKPLLAT 361

Query: 365 EAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQLTA 424
           E++  D  A   L+E     FLA+ A   EVFGP  L+VR     E+  +    +GQLTA
Sbjct: 362 ESSGRD--ASPNLFETTGAQFLADHALGEEVFGPLGLVVRVGSPAEMEELARGFQGQLTA 419

Query: 425 TLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTSVGA 484
           T+ MDA D   ARRL PVLERKAGR+LVNG+PTGVEV D+MVHGGP+PA++N   TSVG 
Sbjct: 420 TIHMDAGDLETARRLRPVLERKAGRVLVNGFPTGVEVVDSMVHGGPYPASTNFGATSVGT 479

Query: 485 TAIERFLRPVCYQDFPDDLLPE 506
            +I RFLRPV YQ+ P+DLLPE
Sbjct: 480 MSIRRFLRPVAYQNMPEDLLPE 501


Lambda     K      H
   0.320    0.137    0.396 

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: 850
Number of extensions: 42
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: 525
Length of database: 505
Length adjustment: 35
Effective length of query: 490
Effective length of database: 470
Effective search space:   230300
Effective search space used:   230300
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: 52 (24.6 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