GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sinorhizobium meliloti 1021

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate SMa0805 SMa0805 GabD4 succinate-semialdehyde dehdyrogenase

Query= metacyc::MONOMER-15736
         (480 letters)



>FitnessBrowser__Smeli:SMa0805
          Length = 490

 Score =  612 bits (1578), Expect = e-180
 Identities = 297/482 (61%), Positives = 372/482 (77%), Gaps = 2/482 (0%)

Query: 1   MQLKDAQLFRQQAFIDGAWVD-ADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADK 59
           ++LKD  L   +  I   W+D +D+G+T  V+NPATGE++  +P M  +ET RAI+AA  
Sbjct: 9   VKLKDPSLAVDKGLIGAEWLDRSDSGKTFDVSNPATGEVIAILPDMSRSETARAIDAAHA 68

Query: 60  ALPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWF 119
           A  AW   T KERA  LR  Y+L++ N DDL  ++T+E GKPL EAKGEI Y AS++EWF
Sbjct: 69  AQRAWAEKTGKERAAVLRNLYDLVVANADDLATILTMEMGKPLTEAKGEILYGASYVEWF 128

Query: 120 AEEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVI 179
            EEAKR+YGD IPGHQPDKR+IV+KQPIGV AAITPWNFP AM+ RK  PA AAGC +V 
Sbjct: 129 GEEAKRVYGDTIPGHQPDKRIIVLKQPIGVVAAITPWNFPNAMLARKLAPAAAAGCAVVS 188

Query: 180 KPASQTPFSALALVELAHRAGIPKGVLSVVTGS-AGDIGGELTSNPIVRKLSFTGSTEIG 238
           KPA++TP SALAL  LA RAG+P GV +V+  + + ++G E+ +N  VRKL+FTGST +G
Sbjct: 189 KPAAETPLSALALALLAERAGLPAGVFNVILSTDSAEVGKEMCANDKVRKLTFTGSTNVG 248

Query: 239 RQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQ 298
           + LM + A  I K+ LELGGNAPFIVFDDADLD AVEGA+++KYRNNGQTCVCANR+++Q
Sbjct: 249 KILMRQGADQIMKLGLELGGNAPFIVFDDADLDAAVEGAMVAKYRNNGQTCVCANRIFVQ 308

Query: 299 DSVYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGG 358
             +YDAFA +L A V+++ IG+G E     GPLI EKA+AKV+EHI DA+ KGA L+ GG
Sbjct: 309 AGIYDAFAARLTAKVSEMTIGDGFEPDVDAGPLISEKALAKVEEHIRDAVTKGADLVLGG 368

Query: 359 KSMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            +  G FFEPT+L     D  +A EETFGP+APLF+F+ E EV++M+N TEFGLASYFY+
Sbjct: 369 NARGGLFFEPTVLTGATMDMKIAGEETFGPVAPLFKFETENEVVSMANKTEFGLASYFYS 428

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           +D+ +VFRVAEALEYGMVG+NTGLIS EVAPFGG+K SG GREGSKYGI+DY+E KYLCL
Sbjct: 429 KDVSKVFRVAEALEYGMVGINTGLISTEVAPFGGVKQSGQGREGSKYGIDDYVETKYLCL 488

Query: 479 GI 480
            I
Sbjct: 489 SI 490


Lambda     K      H
   0.317    0.135    0.390 

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: 686
Number of extensions: 18
Number of successful extensions: 2
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: 480
Length of database: 490
Length adjustment: 34
Effective length of query: 446
Effective length of database: 456
Effective search space:   203376
Effective search space used:   203376
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 (21.7 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