GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dinoroseobacter shibae DFL-12

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::C6KEM4
         (506 letters)



>FitnessBrowser__Dino:3609634
          Length = 780

 Score =  311 bits (796), Expect = 7e-89
 Identities = 191/479 (39%), Positives = 273/479 (56%), Gaps = 38/479 (7%)

Query: 9   RRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAAR---DAFSRDGG 65
           R G+FIGG ++ P  G+     NPA    +  +  GT  D+E AV AAR    A++R GG
Sbjct: 32  RFGVFIGGTFQAP--GKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGG 89

Query: 66  RQWSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAAC--FEYY 123
           + W+R         L AIA  ++      A+LETLD+GKP+ E S D+D   A   F Y+
Sbjct: 90  QGWARV--------LYAIARLLQKHSRLFAVLETLDNGKPIRE-SRDIDIPLAQRHFYYH 140

Query: 124 ADLAEALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCT 183
           A +A  ++ +    +              P+GV G I PWN+PLLM  WK+APALA G T
Sbjct: 141 AGMAALMEDELPDRV--------------PVGVCGQIVPWNFPLLMLAWKIAPALAMGNT 186

Query: 184 TILKPSELASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTE 243
            +LKP+E   ++ L    IC E G+PPGV+NI+TG G   GA L SH  VDK+AFTGST+
Sbjct: 187 VVLKPAEWTPLTALLFAEICGEAGVPPGVVNIVTGDG-ATGAALVSHPGVDKIAFTGSTD 245

Query: 244 TGKRIMTSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRL 303
            G+ I  + A   K ++LELGGKSP +VF+D  D+D AVE  +  I+ N GQVC A SRL
Sbjct: 246 VGREIRRATAGTGKALTLELGGKSPYVVFED-ADLDSAVEGLVDAIWFNQGQVCCAGSRL 304

Query: 304 LLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATIL 363
           L+ E IA+ F  +L A    +++ DPL++   +G+++      K+ + ++ +  E   + 
Sbjct: 305 LVQEGIAEAFYAKLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGE---VH 361

Query: 364 YGGGRPQHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423
             G  P     G F  PT+IT +  +  + ++E+FGPV+    FRT +EAVE+AN T YG
Sbjct: 362 QPGTVP---AEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYG 418

Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNY 482
           LA  + S +  R   I+  L +G++W+N +      A +GG + SGFGRE G  GL  Y
Sbjct: 419 LAATLWSENINRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAY 477



 Score = 92.8 bits (229), Expect = 4e-23
 Identities = 79/281 (28%), Positives = 119/281 (42%), Gaps = 15/281 (5%)

Query: 12  LFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRA 71
           ++IGG    P  G   PV +P     +G  P G+ +D+  AV AA  A S      W R 
Sbjct: 510 MYIGGKQARPDSGYSRPVWSPKG-VLLGHAPEGSRKDIRNAVEAATGAAS------WGRT 562

Query: 72  PGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAEALD 131
            G +RA  L  +A  +  R  E A      +G  +  A  ++         YA  A+  D
Sbjct: 563 TGHLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYD 622

Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191
           G  +    +P+    +  + EP+GV+G   P + PLL A   +  ALA G   +L PSE 
Sbjct: 623 GAVKP---VPIRGV-ALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEP 678

Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251
             ++  +L  +     +P GV+NI+TG       PL+SH  VD V      +    I   
Sbjct: 679 FPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEAE 738

Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGDIDKAVE----WTMFG 288
           AA  +K   +  G     +  D    + +A E    W  +G
Sbjct: 739 AAGNLKRTWVNHGRARDWMQVDARSFLAQATETKTIWVPYG 779


Lambda     K      H
   0.318    0.136    0.418 

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: 1050
Number of extensions: 40
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 506
Length of database: 780
Length adjustment: 38
Effective length of query: 468
Effective length of database: 742
Effective search space:   347256
Effective search space used:   347256
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: 54 (25.4 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