GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pseudomonas putida KT2440

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate PP_1949 PP_1949 Oxidoreductase, GMC family

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__Putida:PP_1949 PP_1949 Oxidoreductase, GMC
           family
          Length = 550

 Score =  389 bits (1000), Expect = e-112
 Identities = 223/535 (41%), Positives = 315/535 (58%), Gaps = 26/535 (4%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           +DY+I+GAGSAGCVLANRLSA+P  +V LLEAG   +      P G++ ++     NWA+
Sbjct: 8   YDYIIIGAGSAGCVLANRLSANPEHSVLLLEAGSRPKGLWASMPAGVSRVILPGPTNWAY 67

Query: 63  KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122
           ++ P P L GR  Y PRGK LGGSS+INGM Y+RGH++D++ W +LG  GWG+DDVLP++
Sbjct: 68  QSEPDPSLAGRRIYVPRGKALGGSSAINGMAYLRGHREDYDHWVSLGCAGWGWDDVLPFY 127

Query: 123 RKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181
           +K E    G   + G DGEL+V+ P  +H +S+AF+ES + AG     D N  + EG G+
Sbjct: 128 KKFEHREEGDEAFRGRDGELWVTDPVFKHPSSQAFIESCVEAGIPRLDDLNAPSPEGTGF 187

Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241
              TI+ GRR S ATAFL+PV  R NL VLT   V+ IV+  ++ATGV+  + G++    
Sbjct: 188 LQFTIKGGRRHSAATAFLQPVLKRPNLHVLTGALVQKIVIEAERATGVEYSL-GNQSIFA 246

Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301
           A +E+ILSAGA  SP LLMLSG+G A EL   GI    +LPGVG+NL DH  V    +++
Sbjct: 247 AAREIILSAGAIDSPKLLMLSGVGPAQELTRHGIPVLRDLPGVGENLHDHVYVHSGIETD 306

Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361
             + L   L G   + + M +Y     G +    ++A A  +  PG  RPD Q+      
Sbjct: 307 RVASLNKDLRGLRSVLQGM-NYLLRGKGCLTMGASQAVALAQVLPGARRPDTQI------ 359

Query: 362 VDDHNRKLHW------------GHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLA 409
              + R L W             +  +   C L P S G + L S +P  AP I PN+  
Sbjct: 360 ---NYRPLSWHFNKQGLVEIGKDNAVTISTCQLNPLSRGRLTLKSSNPIDAPAIYPNYFG 416

Query: 410 HDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKR-TDTIYHPIG 468
           ++ D+   +   R  R+I    P+A   + ++      +D ++ + +R+    ++ H +G
Sbjct: 417 NERDMVAAIAAVRKVREISCVGPLAKH-IVNISPPDSMSDGEIADYIRQEGASSMMHWVG 475

Query: 469 TCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           +CKMG D MAVVD +L+V G++GLRVVDASIMPT+  GNTNA  IMI E+ A  I
Sbjct: 476 SCKMGIDSMAVVDERLKVRGLQGLRVVDASIMPTITSGNTNAPTIMIGEKGAAMI 530


Lambda     K      H
   0.319    0.137    0.419 

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: 777
Number of extensions: 39
Number of successful extensions: 6
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: 526
Length of database: 550
Length adjustment: 35
Effective length of query: 491
Effective length of database: 515
Effective search space:   252865
Effective search space used:   252865
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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