GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Phaeobacter inhibens BS107

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase

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



>FitnessBrowser__Phaeo:GFF3227
          Length = 802

 Score =  310 bits (793), Expect = 2e-88
 Identities = 189/469 (40%), Positives = 273/469 (58%), Gaps = 22/469 (4%)

Query: 23  FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82
           FINGE+T    G+ FD  +P  G +L  ++    +D   AV+ AR   +   WS    + 
Sbjct: 60  FINGEFT--APGDGFDSKNPATGEVLATLSQATQSDVDSAVDAARKAQTK--WSAAGGAA 115

Query: 83  RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142
           R   +   A L+++HA   A+LETLD GKPI +S +IDVP A +   +       +  E 
Sbjct: 116 RARYLYAIARLMQKHARLFAVLETLDNGKPIRESRDIDVPLAQRHFYYHAGMAQLMESE- 174

Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202
                    L  RE +GV G I+PWNFPL+M  WK+ PA++ GN+VVLKP+E + LTAL 
Sbjct: 175 ---------LPDREALGVCGQIIPWNFPLLMLAWKVAPAIAMGNTVVLKPAEYTSLTALL 225

Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262
            A +  +AG+PKGV+N++ G G  VG+ + +  DVD + FTGST + +++   +  S  K
Sbjct: 226 FADICRQAGLPKGVVNIVTGDG-AVGEMI-VGADVDKIAFTGSTAVGRRIREATAGSG-K 282

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322
            + LE GGKSP IVF DA D+ +A E    AI FNQG+VC AGSRLLV+  I + F   +
Sbjct: 283 ALTLELGGKSPYIVFDDA-DIDSAIEGLVDAIWFNQGQVCCAGSRLLVQEGIAERFHTKL 341

Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETGGTY 382
              +   + GNPLD + +VGA+VD  Q+ T+ S + A ++ G    A   ++     G +
Sbjct: 342 RVRMDKLRIGNPLDKSIDVGAIVDPVQLTTI-SEMVAANTAGRMHQA---QVAVPERGCF 397

Query: 383 VEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAH 442
             PT+ +G++ +  + QEEIFGPVL    F T  +A+E+AN+T YGLAA +WT++++ A 
Sbjct: 398 YPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVELANNTRYGLAATLWTENVNLAL 457

Query: 443 LTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELK 491
             A  L AG VWVN  +  D  A FGG ++SG GR+        YT+ K
Sbjct: 458 DIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGGWEGLSAYTKPK 506



 Score = 79.7 bits (195), Expect = 4e-19
 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 15/245 (6%)

Query: 25  NGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRK 84
           +G Y+ A+  ++        G LLG +   +  D + AVE   A   +  WS+     R 
Sbjct: 544 DGGYSKAIHSKS--------GGLLGHVGLGNRKDVRNAVE---AAAGANAWSKTTGHLRA 592

Query: 85  ATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAA 144
             +      L     E A  + +D     S     +V  + Q L  +    DK   +   
Sbjct: 593 QILYYIGENLSARVGEFA--DRIDRMTGKSQGAQ-EVEASIQRLFTAAAWADKYDGQAHG 649

Query: 145 TPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIA 204
            P   + L  +EPVGV+GA+     PL+     + PA++ GN VVL  SE  PL+A    
Sbjct: 650 VPIRGVALAMKEPVGVIGALCADEAPLLGLVSVMAPAIAMGNRVVLAASEAYPLSATDFY 709

Query: 205 ALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRI 264
            +   + +P GV+N+L G    +   LA H++VD  V++ S+     ++  +   N+KR 
Sbjct: 710 QVLETSDLPGGVVNILTGRHAEMASPLASHLNVDA-VWSFSSSDLSAMIEEASAGNLKRT 768

Query: 265 WLEAG 269
           W+  G
Sbjct: 769 WVNNG 773


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: 1024
Number of extensions: 53
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 497
Length of database: 802
Length adjustment: 38
Effective length of query: 459
Effective length of database: 764
Effective search space:   350676
Effective search space used:   350676
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