GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Sinorhizobium meliloti 1021

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate SMa0805 SMa0805 GabD4 succinate-semialdehyde dehdyrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__Smeli:SMa0805 SMa0805 GabD4
           succinate-semialdehyde dehdyrogenase
          Length = 490

 Score =  623 bits (1606), Expect = 0.0
 Identities = 308/482 (63%), Positives = 382/482 (79%), Gaps = 4/482 (0%)

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

Query: 60  ALPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWF 119
           A  AW   T KERA  LR  +DL++ N DDLA ++T+E GKPL EAKGEI Y AS++EWF
Sbjct: 69  AQRAWAEKTGKERAAVLRNLYDLVVANADDLATILTMEMGKPLTEAKGEILYGASYVEWF 128

Query: 120 GEEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVL 179
           GEEAKR+YGDTIPGHQPDKRIIV+KQPIGV AAITPWNFP+AM+ RK  PA AAGC +V 
Sbjct: 129 GEEAKRVYGDTIPGHQPDKRIIVLKQPIGVVAAITPWNFPNAMLARKLAPAAAAGCAVVS 188

Query: 180 KPASQTPYSALALAELAERAGIPKGVFSVVTGS-AGEVGGELTSNPIVRKLTFTGSTEIG 238
           KPA++TP SALALA LAERAG+P GVF+V+  + + EVG E+ +N  VRKLTFTGST +G
Sbjct: 189 KPAAETPLSALALALLAERAGLPAGVFNVILSTDSAEVGKEMCANDKVRKLTFTGSTNVG 248

Query: 239 RQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQ 298
           + LM + A  I K+ LELGGNAPFIVFDDADLDAAVEGA+++KYRNNGQTCVCANR++VQ
Sbjct: 249 KILMRQGADQIMKLGLELGGNAPFIVFDDADLDAAVEGAMVAKYRNNGQTCVCANRIFVQ 308

Query: 299 DGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGG 358
            G+YDAF  +L A V+++ IG+G E  V  GPLI  KA+AKVEEHI DAV+KGA +V GG
Sbjct: 309 AGIYDAFAARLTAKVSEMTIGDGFEPDVDAGPLISEKALAKVEEHIRDAVTKGADLVLGG 368

Query: 359 KPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYF 418
             +A GG FFEPT+L     +  ++ +ETFGP+AP+F+F+ E EV++M+N TEFGLASYF
Sbjct: 369 --NARGGLFFEPTVLTGATMDMKIAGEETFGPVAPLFKFETENEVVSMANKTEFGLASYF 426

Query: 419 YARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 478
           Y++D+++VFRVAE LEYGMVGINTGLIS EVAPFGG+K SG GREGSKYGI+DY+E KYL
Sbjct: 427 YSKDVSKVFRVAEALEYGMVGINTGLISTEVAPFGGVKQSGQGREGSKYGIDDYVETKYL 486

Query: 479 CL 480
           CL
Sbjct: 487 CL 488


Lambda     K      H
   0.317    0.135    0.391 

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: 711
Number of extensions: 17
Number of successful extensions: 3
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: 483
Length of database: 490
Length adjustment: 34
Effective length of query: 449
Effective length of database: 456
Effective search space:   204744
Effective search space used:   204744
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 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