GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011383257.1 AMB_RS04160 NAD-dependent
           succinate-semialdehyde dehydrogenase
          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.

Links

Downloads

Related tools

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 preprint 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