GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Cupriavidus basilensis 4G11

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate RR42_RS21375 RR42_RS21375 succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15736
         (480 letters)



>FitnessBrowser__Cup4G11:RR42_RS21375
          Length = 488

 Score =  684 bits (1766), Expect = 0.0
 Identities = 342/484 (70%), Positives = 393/484 (81%), Gaps = 5/484 (1%)

Query: 1   MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           MQLKD  L R QAFI G W  AD+G T  V NPA G ++GTVP MGAAET RAIEAA  A
Sbjct: 1   MQLKDPTLLRSQAFIGGQWQSADSGATFPVTNPADGSLIGTVPLMGAAETTRAIEAARVA 60

Query: 61  LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120
             AWR  TA+ERA  LR WY+L++ N DDL  LMT EQGKPLAEA+GE  YAASF+EWFA
Sbjct: 61  QAAWRRKTARERAQVLRAWYDLMLANADDLAVLMTTEQGKPLAEARGEAVYAASFLEWFA 120

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           E+AKR++GDV+     DKRL+V+K+P+GV AAITPWNFP AMITRKAGPALAAGC MV+K
Sbjct: 121 EQAKRVHGDVLATPASDKRLLVVKEPVGVCAAITPWNFPLAMITRKAGPALAAGCAMVLK 180

Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAG---DIGGELTSNPIVRKLSFTGSTEI 237
           PA  TP SALAL  LA RAG+P G+LSVVTG A    +IG ELT +P+VRKLSFTGSTE+
Sbjct: 181 PAEDTPLSALALALLAERAGLPAGLLSVVTGDAASSIEIGAELTGSPVVRKLSFTGSTEV 240

Query: 238 GRQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYI 297
           GR LM + A  IKK+SLELGGNAPFIVFDDADLD AVEGA+ SKYRN GQTCVCANRLY+
Sbjct: 241 GRILMRQSAPTIKKLSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYV 300

Query: 298 QDSVYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAG 357
            D VYDAFA+KL AAV  LK+G+GLE G   GPLI+E AVAKV++HIADAL KGA LL G
Sbjct: 301 HDKVYDAFAQKLVAAVKTLKVGHGLEPGVQQGPLINEDAVAKVEQHIADALGKGARLLTG 360

Query: 358 GK--SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASY 415
           GK   + G FFEPT+L NV  D  VAK+ETFGPLAPLFRF  + EV+ M+NDTEFGLASY
Sbjct: 361 GKRHDLGGTFFEPTVLANVTPDMVVAKQETFGPLAPLFRFTSDEEVVNMANDTEFGLASY 420

Query: 416 FYARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 475
           F++RD+GR++RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREG+ YGIE+YLE+KY
Sbjct: 421 FFSRDIGRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGASYGIEEYLEVKY 480

Query: 476 LCLG 479
           LC+G
Sbjct: 481 LCMG 484


Lambda     K      H
   0.317    0.135    0.390 

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: 726
Number of extensions: 16
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: 480
Length of database: 488
Length adjustment: 34
Effective length of query: 446
Effective length of database: 454
Effective search space:   202484
Effective search space used:   202484
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