GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Sinorhizobium meliloti 1021

Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate SMc00985 SMc00985 oxidoreductase

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Smeli:SMc00985
          Length = 480

 Score =  313 bits (803), Expect = 7e-90
 Identities = 169/441 (38%), Positives = 261/441 (59%), Gaps = 15/441 (3%)

Query: 98  YKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFD--ELILSLANL 155
           Y+G + LVLRP SVE+VSL++   +  + AVVPQGGNTG V G +P     +++LSL  L
Sbjct: 41  YRGTTPLVLRPGSVEEVSLVMRLASQTRTAVVPQGGNTGHVAGQIPREGKADVVLSLERL 100

Query: 156 NKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGGLRL 215
           N+IRD DPV  ++  DAG IL +      + + +FPL LG++GS  +GG ++TNAGG  +
Sbjct: 101 NRIRDIDPVGNVIVADAGCILADIQKAADDVDRLFPLSLGSEGSARIGGNLSTNAGGTAV 160

Query: 216 LRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSILTV 275
           L YG++    LGLEVV+P G+I + +  +RKDNTGYDL+ LFIG+EGT+G+ITG  +   
Sbjct: 161 LAYGNMRQLCLGLEVVLPTGEIWDGLRRLRKDNTGYDLRDLFIGAEGTLGVITGAVLKLF 220

Query: 276 PKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDAAFPLE 335
           PKP+   V++  + S ED   +F RA       L+ FE M           +     P+E
Sbjct: 221 PKPRGHQVAFAGLRSVEDALTLFDRATSVCGPALTGFELMPRLGIEFTTRHIAGVRDPME 280

Query: 336 DEHPFYILIETSGSN-KDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWREMIP 394
             HP+Y LI+ S S+  +  +  ++  LE V+ +G+V + V+AQ+E + + LW  RE + 
Sbjct: 281 TTHPWYALIDISTSDTAESAERMVQDLLEAVIADGLVENAVIAQNEAQRRALWHMRESMS 340

Query: 395 EASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGDGNLH 454
            A +  GG  K+DVS+P       V +  A ++EA+ +     P      +GH+GDGN+H
Sbjct: 341 PAQKPEGGSIKHDVSVP-------VSSIPAFMTEADALVSKAIPGARICAFGHMGDGNIH 393

Query: 455 LNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVK 509
            N+     A ++   +  + +   V+  V    GS+SAEHG+G  K++ +   +SP E++
Sbjct: 394 YNISQPVGADKQSFLDRWREINAIVHAVVLKHDGSISAEHGIGQLKRDELAAIRSPIEIE 453

Query: 510 MMKDLKVHYDPNGILNPYKYI 530
           +M+ +K  +DP GI+NP K +
Sbjct: 454 LMRRIKHAFDPAGIMNPDKVL 474


Lambda     K      H
   0.316    0.135    0.385 

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: 553
Number of extensions: 18
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: 530
Length of database: 480
Length adjustment: 34
Effective length of query: 496
Effective length of database: 446
Effective search space:   221216
Effective search space used:   221216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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