GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens FW300-N2C3

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate AO356_26740 AO356_26740 succinate-semialdehyde dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_26740
          Length = 485

 Score =  595 bits (1535), Expect = e-175
 Identities = 292/479 (60%), Positives = 369/479 (77%), Gaps = 1/479 (0%)

Query: 2   QLKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKAL 61
           +LKD  L  ++A+IDG WV ADN  T+ V NPATGE+L  VP +  +ETRRA+EAAD+A 
Sbjct: 5   RLKDPSLLVERAYIDGQWVGADNAATVDVINPATGEVLARVPAIQGSETRRAVEAADRAW 64

Query: 62  PAWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAE 121
           PAWRA  A ERA  L RWY+ +I+N DDLA ++T EQGKPLAEA+GEI Y ASF++WFAE
Sbjct: 65  PAWRARPAAERAALLDRWYQAMIDNLDDLALILTCEQGKPLAEAQGEIRYGASFVKWFAE 124

Query: 122 EAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
           EA+R+YG+ I     D+RL+ +KQP+GV AAITPWNFP AMITRK  PALAAGCT+V+KP
Sbjct: 125 EARRVYGETIQAPSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCTIVVKP 184

Query: 182 ASQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQL 241
           +  TP SA ALA LA+R GIPAGVF+VV+G    IG ELT NP VRKLSFTGST +GR L
Sbjct: 185 SDLTPLSALALAVLAERVGIPAGVFNVVTGMPAGIGEELTGNPTVRKLSFTGSTAVGRLL 244

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

Query: 302 YDAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM 361
           Y+ FA++L   V KLK+G+GL+AG   GPLI+  AV+KV  HI +ALS+GA +L G  P 
Sbjct: 305 YERFAQRLVEEVGKLKVGDGLDAGVNIGPLINTAAVSKVARHIDEALSQGARLLCGEIPK 364

Query: 362 -EGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420
            +  F +PT+L        +A EETFGP+APL RF  E + +A +N T +GLA+YF+ +D
Sbjct: 365 GDSQFVQPTVLGEAHAGMLLANEETFGPVAPLMRFSTEEEALASANATPYGLAAYFFTQD 424

Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479
           L R +R  EALE+GMVG+NTGLIS +VAPFGGIK SGLGREGSKYG++++LE+K   +G
Sbjct: 425 LRRSWRFGEALEFGMVGLNTGLISMDVAPFGGIKQSGLGREGSKYGLDEFLEVKAFHMG 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: 678
Number of extensions: 21
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 (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