GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Sinorhizobium fredii NGR234

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_012709840.1 NGR_RS27930 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_000018545.1:WP_012709840.1
          Length = 484

 Score =  215 bits (547), Expect = 3e-60
 Identities = 141/449 (31%), Positives = 222/449 (49%), Gaps = 10/449 (2%)

Query: 71  PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130
           PA  E I RV +   A+ +  ++ A    K WA   A +R  I+R+  + + E    LG 
Sbjct: 33  PATGEIIGRVPKLGAAETKVAIETAARVQKEWAGRTAKERAAILRRWYELMIENKDDLGQ 92

Query: 131 LVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVGI 190
           ++++E GK L E  GE+       ++     R + G ++P  +    ++    P+G+V  
Sbjct: 93  ILTIEQGKPLAEATGEIVYGASFIEWFAEEGRRVYGDLVPGHQKDKRILVMKQPIGVVAA 152

Query: 191 ITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICSL 250
           IT +NFP A+       A   G   + K A  T   ++A    IA + E   +P  + S+
Sbjct: 153 ITPWNFPNAMITRKAGPAFAAGCAMVLKPAAQTPYSAIA----IAVLAERAGMPKGLFSV 208

Query: 251 TCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAIIAFEDA 309
             G A +IG  M  +  V  L+FTGST+VG ++         +  LELGGN   I F+DA
Sbjct: 209 ITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLGLELGGNAPFIVFDDA 268

Query: 310 DLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVLY 369
           DL   V  AL A     GQ C  A RL++ E ++D    +L  A A+++ GN  +   + 
Sbjct: 269 DLDAAVEGALIAKFRNNGQTCVCANRLYVQEGVYDAFSEKLAAAVAKLKTGNGMEDGTIL 328

Query: 370 GPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETF 429
           GPL  K A+      V +A  +G  V+ GG+     G++ E T++  +    ++A  ETF
Sbjct: 329 GPLIDKPALEKVEEHVADALAKGARVIQGGRRHALGGSFFEATVLADVTQAMAVAREETF 388

Query: 430 APILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIP-TS 488
            P+  +F+FK+E +V    N+ + GL+S  + KDL R+FR    +  + G+V VN    S
Sbjct: 389 GPVAPLFRFKDEADVIRQANDTEFGLASYFYAKDLARVFR--VAEALEYGMVGVNTGLIS 446

Query: 489 GAEIGGAFGGEKHTGGGRESGSDAWKQYM 517
            AE    FGG K +G GRE      +++M
Sbjct: 447 TAE--APFGGVKFSGLGREGSKYGIEEFM 473


Lambda     K      H
   0.318    0.136    0.417 

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: 689
Number of extensions: 39
Number of successful extensions: 4
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: 539
Length of database: 484
Length adjustment: 35
Effective length of query: 504
Effective length of database: 449
Effective search space:   226296
Effective search space used:   226296
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