GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Herbaspirillum seropedicae SmR1

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate HSERO_RS16560 HSERO_RS16560 2-hydroxyacid dehydrogenase

Query= BRENDA::Q8N465
         (521 letters)



>FitnessBrowser__HerbieS:HSERO_RS16560
          Length = 468

 Score =  292 bits (747), Expect = 2e-83
 Identities = 178/456 (39%), Positives = 253/456 (55%), Gaps = 20/456 (4%)

Query: 78  VVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVG 137
           V+TD         D      G +  +LRP  S EV+ ++R C +  + + PQGGNTG+V 
Sbjct: 17  VLTDAHDTAGYLTDQRGRYTGRALAVLRPADSAEVAAVVRLCAQFAVPLVPQGGNTGLVL 76

Query: 138 GSVP--VFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAK 195
           GSVP    + ++LS  R+NR+ +  +++  +  ++GCVL+ L         + PL L A+
Sbjct: 77  GSVPDQQGNAVVLSLRRLNRIRAVDALNNTITVESGCVLQHLQEQAAAAGRLFPLSLAAE 136

Query: 196 GSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLF 255
           GSC IGGN++TNAGG   LRYG+     LGLEVV A G ++  L  LRKDNTGYDL+ LF
Sbjct: 137 GSCTIGGNLSTNAGGTGVLRYGNTRELCLGLEVVTAQGEIMSSLKGLRKDNTGYDLRDLF 196

Query: 256 IGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDA 315
           IG+EGTLG+IT   +   P+PRA   A    P  A+ LQ     +   G  L+ FE M  
Sbjct: 197 IGAEGTLGVITAAVMKLFPQPRAQVTALAALPHPAQALQLLQLAQAHCGPALTGFELMSD 256

Query: 316 VCMQLVGRHLHLASPVQESPF------YVLIETSGSNAGHDAEKLGH-FLEHALGSGLVT 368
            C+QLV +H     P Q  PF      YVL+E S S +   A  L    +  AL  GLV 
Sbjct: 257 FCLQLVRKHF----PEQRLPFDRPHPQYVLLELSDSESEEHARALFEGLIGTALEQGLVD 312

Query: 369 DGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIV--TDLRARLGPHA 426
           D  +A    + + LW LRE I+ A + +G   K+D+S+P+ R+ + +  TD+  +     
Sbjct: 313 DAVIAASLAQSRALWRLRESISSAQAHEGKNIKHDISVPISRIAEFIAATDVLVQQAAPG 372

Query: 427 KHVVGYGHLGDGNLHLNVT-----AEAFSPSLLAALEPHVYEWTAGQQGSVSAEHGVGFR 481
             +V +GHLGDGNLH NV+     A+    +  AA+   V++      GS+SAEHG+G  
Sbjct: 373 CRMVTFGHLGDGNLHYNVSPPEGVADRDFIARQAAINRVVHDSVDRFGGSISAEHGLGAL 432

Query: 482 KRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517
           KR+ +   K P  LQLM+ +K  LDP+ ++NP K L
Sbjct: 433 KREEITRYKSPVELQLMRAIKLALDPQQLMNPGKVL 468


Lambda     K      H
   0.321    0.139    0.426 

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: 666
Number of extensions: 41
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: 521
Length of database: 468
Length adjustment: 34
Effective length of query: 487
Effective length of database: 434
Effective search space:   211358
Effective search space used:   211358
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:

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