GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1949
          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:

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