GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pseudomonas putida KT2440

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate PP_4422 PP_4422 succinate-semialdehyde dehydrogenase (NADP+)

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__Putida:PP_4422
          Length = 490

 Score =  494 bits (1273), Expect = e-144
 Identities = 245/480 (51%), Positives = 324/480 (67%), Gaps = 2/480 (0%)

Query: 2   KLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRAL 61
           KL  ++L   +A I+G W+      ++DVT+PAN   +  V          A++AA+RA 
Sbjct: 11  KLRRNDLLETRAYIDGRWVTGEG--SLDVTDPANDQVIAQVAHCDESWVDLAVEAASRAF 68

Query: 62  PAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAE 121
             WR     +R  +LR W  LM E+Q+DLA +MT EQGKPL+E++GEI+Y A+F+EWFA 
Sbjct: 69  DGWRNTLPTQRGAVLRKWAALMRENQEDLAVIMTCEQGKPLSESRGEINYGANFVEWFAA 128

Query: 122 EGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
           EG+R YG+TIP H  + +L+   QPIGVT AITPWNFP+AMITRKA  ALAAGC M++KP
Sbjct: 129 EGERCYGETIPSHLPNSQLVTKLQPIGVTVAITPWNFPSAMITRKAAAALAAGCPMIVKP 188

Query: 182 ASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQL 241
           A +TP SALALA LA  AG+P GVF V+TG A  +   L +   VR  SFTGSTE+GR L
Sbjct: 189 APETPLSALALARLAEEAGIPGGVFQVLTGDAPKMSARLLAASAVRAFSFTGSTEVGRIL 248

Query: 242 MEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGV 301
           + Q A  +KKVSLELGG+APFIVFDDA + +AVEG + +KF  +GQ C+ ANR+YV   +
Sbjct: 249 LRQSADTVKKVSLELGGHAPFIVFDDASIAEAVEGCIGAKFATSGQDCLGANRIYVHRNI 308

Query: 302 YDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361
           Y +F E+  +A  KL +G GL+ GV IGP+       K  E I++AL  GA++ CGG  +
Sbjct: 309 YGQFVEEFTKATEKLRVGHGLEEGVDIGPMTRVTVANKCREQISNALSLGAKLTCGGIDN 368

Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421
             G +F  PT+L DV     ++ EETFGP+A +  F  E +V+ +AN+TEFGLAAY Y  
Sbjct: 369 HLGSSFVLPTVLADVTDKMDIAFEETFGPVAAILPFDSEDEVVTRANNTEFGLAAYVYTN 428

Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           DL R  RV + LEYG+V +NT   +    PFGG K SGLGREGSK+G+ +Y+E+KY+CIG
Sbjct: 429 DLRRACRVSDRLEYGMVALNTPKFTGAPIPFGGWKQSGLGREGSKHGLAEYMELKYVCIG 488


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: 622
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: 490
Length adjustment: 34
Effective length of query: 448
Effective length of database: 456
Effective search space:   204288
Effective search space used:   204288
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