GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pseudomonas fluorescens FW300-N2E3

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate AO353_28230 AO353_28230 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_28230
          Length = 485

 Score =  604 bits (1557), Expect = e-177
 Identities = 295/480 (61%), Positives = 367/480 (76%), Gaps = 1/480 (0%)

Query: 2   KLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRAL 61
           +L D +L  + A I+G+W+ A+N   +DV +PANG  L  VP M   ETR AIDAA +A 
Sbjct: 5   RLKDPSLLAELAYIDGQWIGADNAATLDVIDPANGQLLARVPAMQGTETRRAIDAAEKAW 64

Query: 62  PAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAE 121
           PAWRA  A ERA +L  W+  M+++ DDLA +MT EQGKPL EAKGEI Y A F++WFAE
Sbjct: 65  PAWRARPAAERAALLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAE 124

Query: 122 EGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
           E +R+YG+TIP    D+RL+ +KQP+GV AAITPWNFP AMITRK  PALAAGC +++KP
Sbjct: 125 EARRVYGETIPAPSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKP 184

Query: 182 ASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQL 241
           +  TP SALALA LA R G+PAGVFNV+TG    +G ELT NP VRK+SFTGST +GR L
Sbjct: 185 SDLTPLSALALAVLAERVGIPAGVFNVLTGMPAGIGEELTGNPSVRKISFTGSTAVGRLL 244

Query: 242 MEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGV 301
           M Q A+ IK++SLELGGNAPFIVFDDADL++AV G + SKFRNAGQTCVCANR+ VQDG+
Sbjct: 245 MRQSAEHIKRLSLELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGI 304

Query: 302 YDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361
           Y+RFA++L + V KL +G+GLD  VTIGPLI+  AV+KV  HI DAL +GAR++CGG   
Sbjct: 305 YERFAQRLVEEVGKLKVGNGLDADVTIGPLINPAAVSKVARHIDDALSQGARLLCGG-IP 363

Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421
           E    F QPT+L D  A   ++ EETFGP+APL RF +EA+ +A AN T +GL AY++ +
Sbjct: 364 EGDSQFVQPTVLGDAHAGMLLANEETFGPVAPLMRFTEEAEALALANATPYGLGAYYFTQ 423

Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           DL R +R GEALE+G+VG+NTGIIS EVAPFGGIK SGLGREGSKYG+++YLE+K   IG
Sbjct: 424 DLRRSWRFGEALEFGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKAFHIG 483


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: 754
Number of extensions: 27
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: 482
Length of database: 485
Length adjustment: 34
Effective length of query: 448
Effective length of database: 451
Effective search space:   202048
Effective search space used:   202048
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