GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Sinorhizobium fredii NGR234

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_012709840.1 NGR_RS27930 NADP-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_000018545.1:WP_012709840.1
          Length = 484

 Score =  723 bits (1866), Expect = 0.0
 Identities = 350/483 (72%), Positives = 410/483 (84%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           M LKD  LFRQ A V   W++AD    I+VNNPATGEIIG VPK+GAAET+ AIE A + 
Sbjct: 1   MNLKDPSLFRQAALVGENWIEADPQNAIEVNNPATGEIIGRVPKLGAAETKVAIETAARV 60

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
              W   TAKERA  LRRW++LMIEN+DDL +++TIEQGKPLAEA GEI Y ASF+EWF 
Sbjct: 61  QKEWAGRTAKERAAILRRWYELMIENKDDLGQILTIEQGKPLAEATGEIVYGASFIEWFA 120

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EE +R+YGD +PGHQ DKRI+V+KQPIGV AAITPWNFP+AMITRKAGPA AAGC MVLK
Sbjct: 121 EEGRRVYGDLVPGHQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPAFAAGCAMVLK 180

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           PA+QTPYSA+A+A LAERAG+PKG+FSV+TGSA E+G E+TSNP VRKLTFTGSTE+G +
Sbjct: 181 PAAQTPYSAIAIAVLAERAGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAE 240

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           L  + A  IKK+ LELGGNAPFIVFDDADLDAAVEGALI+K+RNNGQTCVCANRLYVQ+G
Sbjct: 241 LYRQSAATIKKLGLELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRLYVQEG 300

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYDAF +KL AAVAKL  GNG+E G   GPLID  A+ KVEEH+ADA++KGA+V+ GG+ 
Sbjct: 301 VYDAFSEKLAAAVAKLKTGNGMEDGTILGPLIDKPALEKVEEHVADALAKGARVIQGGRR 360

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           HALGG+FFE T+L DV +   V+++ETFGP+AP+FRFKDEA+VI  +NDTEFGLASYFYA
Sbjct: 361 HALGGSFFEATVLADVTQAMAVAREETFGPVAPLFRFKDEADVIRQANDTEFGLASYFYA 420

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           +DLARVFRVAE LEYGMVG+NTGLIS   APFGG+K SGLGREGSKYGIE+++EIKY+CL
Sbjct: 421 KDLARVFRVAEALEYGMVGVNTGLISTAEAPFGGVKFSGLGREGSKYGIEEFMEIKYVCL 480

Query: 481 GGI 483
           GGI
Sbjct: 481 GGI 483


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: 755
Number of extensions: 18
Number of successful extensions: 1
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: 484
Length adjustment: 34
Effective length of query: 449
Effective length of database: 450
Effective search space:   202050
Effective search space used:   202050
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 Apr 09 2024. 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