GapMind for catabolism of small carbon sources

 

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

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>FitnessBrowser__Dino:3609634
          Length = 780

 Score =  305 bits (782), Expect = 3e-87
 Identities = 189/472 (40%), Positives = 262/472 (55%), Gaps = 33/472 (6%)

Query: 23  FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82
           FI G +     G+TF   +P  G  L ++     AD + AV  AR   +   W+RL    
Sbjct: 36  FIGGTFQ--APGKTFATRNPARGTELAQVTQGTEADIEAAVTAARR--AQPAWARLGGQG 91

Query: 83  RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142
               +   A LL++H+   A+LETLD GKPI +S +ID+P A +   +       + DE 
Sbjct: 92  WARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDE- 150

Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202
                    L  R PVGV G IVPWNFPL+M  WK+ PAL+ GN+VVLKP+E +PLTAL 
Sbjct: 151 ---------LPDRVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALL 201

Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262
            A +  EAG+P GV+N++ G G T G AL  H  VD + FTGST + +++   +  +  K
Sbjct: 202 FAEICGEAGVPPGVVNIVTGDGAT-GAALVSHPGVDKIAFTGSTDVGREIRRATAGTG-K 259

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322
            + LE GGKSP +VF DA DL +A E    AI FNQG+VC AGSRLLV+  I + F   +
Sbjct: 260 ALTLELGGKSPYVVFEDA-DLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKL 318

Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETG--- 379
              +   + G+PLD   +VGA+VD      V           A++VAG    + + G   
Sbjct: 319 RARMATLRIGDPLDKCIDVGAMVDPAHCAKV-----------AEMVAGSNGEVHQPGTVP 367

Query: 380 --GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKD 437
             G +  PT+  G+  A  + ++EIFGPVL    F T  +A+E+AN T YGLAA +W+++
Sbjct: 368 AEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSEN 427

Query: 438 ISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTE 489
           I++A   A  L AG VWVN  +  D  A FGG ++SG GR+        YT+
Sbjct: 428 INRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479



 Score = 87.8 bits (216), Expect = 1e-21
 Identities = 75/249 (30%), Positives = 104/249 (41%), Gaps = 6/249 (2%)

Query: 21  RAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAP 80
           + +I G+     SG +    SP  G LLG        D + AVE A    S   W R   
Sbjct: 509 KMYIGGKQARPDSGYSRPVWSP-KGVLLGHAPEGSRKDIRNAVEAATGAAS---WGRTTG 564

Query: 81  SKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYD 140
             R   +   A  L    EE A       G  +  +   +V  A   L       DK   
Sbjct: 565 HLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRA-EAEVSAAIDRLFTYAAWADKYDG 623

Query: 141 EVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTA 200
            V   P   + L   EPVGV+GA  P + PL+ A   LG AL+ GN +VL PSE  PL A
Sbjct: 624 AVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAA 683

Query: 201 LRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESN 260
             +  +   + +P GV+N++ G    + K LA H+ VD +       I+  +       N
Sbjct: 684 TDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEA-EAAGN 742

Query: 261 MKRIWLEAG 269
           +KR W+  G
Sbjct: 743 LKRTWVNHG 751


Lambda     K      H
   0.316    0.132    0.389 

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: 1039
Number of extensions: 61
Number of successful extensions: 7
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: 497
Length of database: 780
Length adjustment: 37
Effective length of query: 460
Effective length of database: 743
Effective search space:   341780
Effective search space used:   341780
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 (21.6 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