GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Magnetospirillum magneticum AMB-1

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  607 bits (1564), Expect = e-178
 Identities = 300/478 (62%), Positives = 364/478 (76%), Gaps = 1/478 (0%)

Query: 5   DSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAW 64
           D +L +  A ++G W+ A++G   DV +PA G  + SVP +GA ETR AIDAA  A   W
Sbjct: 19  DPSLIKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPW 78

Query: 65  RALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGK 124
           R  TAK+RA ++  W +L+M HQD LARL++ EQGKPLAEA GEISY ASFI WFAEEGK
Sbjct: 79  RQRTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGK 138

Query: 125 RIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQ 184
           R YGD IP   +D+RL+V+KQPIGV AA+TPWNFP AMITRK  PALAAGC +V+KPA  
Sbjct: 139 RAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAED 198

Query: 185 TPFSALALAELAIRAGVPAGVFNVVTG-SAGAVGNELTSNPLVRKLSFTGSTEIGRQLME 243
           TP SALALAELA RAG+P G+FN+VT     AVG E+T N  VRKLSFTGST +G+ LM 
Sbjct: 199 TPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMA 258

Query: 244 QCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYD 303
           QCA+ +KKVSLELGGNAPFIVFDD DLD AV GALASK+RN+GQTC+C NR  VQ G+Y+
Sbjct: 259 QCAETVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYE 318

Query: 304 RFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHER 363
            FA KL +  + + +G  L   V  GPLI+  AVAKV  H+ADA+ KGARV+ GG+ H  
Sbjct: 319 DFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHAL 378

Query: 364 GGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDL 423
           GG F+QPT+L DV       +EETFGP+APL RF+ EA+ IA AN +EFGLA YFY+RD+
Sbjct: 379 GGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRDV 438

Query: 424 SRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           +RVFRV EALE G+VG+N  +ISNEVAPFGGIK SGLGREGSKYG++D++E KY+CIG
Sbjct: 439 ARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVCIG 496


Lambda     K      H
   0.318    0.135    0.395 

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: 722
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: 482
Length of database: 499
Length adjustment: 34
Effective length of query: 448
Effective length of database: 465
Effective search space:   208320
Effective search space used:   208320
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