Alignments for a candidate for kauB in Phaeobacter inhibens BS107

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources