GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas fluorescens FW300-N1B4

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Pf1N1B4_4931 Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.79)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4931
           Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20);
           Succinate-semialdehyde dehydrogenase [NADP+] (EC
           1.2.1.79)
          Length = 485

 Score =  596 bits (1537), Expect = e-175
 Identities = 287/479 (59%), Positives = 370/479 (77%), Gaps = 1/479 (0%)

Query: 2   QLKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKAL 61
           +LKD  L  + A++DG W+ ADN  T+ V +PA+G++L  VP M  A+TRRAIEAA++A 
Sbjct: 5   RLKDPSLLAELAYVDGQWIGADNAATLDVIDPASGQLLARVPAMQGAQTRRAIEAAERAW 64

Query: 62  PAWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAE 121
           PAWRA  A ERA  L RWY+ +I+N DDLA +MT EQGKPL EAKGEI Y A F++WFAE
Sbjct: 65  PAWRARPAAERAALLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAE 124

Query: 122 EAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
           EA+R+YG+ +P    D+RL+ +KQP+GV AAITPWNFP AMITRK  PALAAGC +++KP
Sbjct: 125 EARRVYGETMPAPSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKP 184

Query: 182 ASQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQL 241
           +  TP SA ALA LA+R GIPAGVF+V++G    IG ELT NP VRK+SFTGST +GR L
Sbjct: 185 SDLTPLSALALAVLAERVGIPAGVFNVLTGMPAGIGEELTGNPTVRKISFTGSTAVGRLL 244

Query: 242 MSECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGV 301
           M + A+ IK++SLELGGNAPFIVFDDADL++AV G ++SK+RN GQTCVCANR+ +QDG+
Sbjct: 245 MRQSAEHIKRLSLELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGI 304

Query: 302 YDAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM 361
           Y+ FA++L   V KLK+GNGL+A  T GPLI+  AV+K+  HI DALS+GA +L GG P 
Sbjct: 305 YERFAQRLVEEVGKLKVGNGLDADVTIGPLINPAAVSKIARHIDDALSQGARLLCGGIPE 364

Query: 362 -EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420
            +  F +PT+L +      +A EETFGP+APL RF DEA+ +A++N T +GL +Y++ +D
Sbjct: 365 GDSQFVQPTVLGDTHAGMLLANEETFGPVAPLMRFTDEAEALALANATPYGLGAYYFTQD 424

Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479
           L R +R  EALE+GMVG+NTG+IS EVAPFGGIK SGLGREGSKYG+++YLE+K   +G
Sbjct: 425 LRRSWRFGEALEFGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKAFHIG 483


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: 695
Number of extensions: 22
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: 480
Length of database: 485
Length adjustment: 34
Effective length of query: 446
Effective length of database: 451
Effective search space:   201146
Effective search space used:   201146
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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