Aligments for a candidate for puuC in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for puuC in Herbaspirillum seropedicae SmR1

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS05115
          Length = 793

 Score =  317 bits (813), Expect = 8e-91
 Identities = 188/462 (40%), Positives = 268/462 (58%), Gaps = 31/462 (6%)

Query: 23  FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82
           FI G +T   +    D + P  G+LL  ++    AD   AV+ A+A      W  L    
Sbjct: 36  FIAGRFTQPKAD--LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALPG--WQALGGHG 91

Query: 83  RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQAL----SWSGEAIDKL 138
           R   +   A  +++HA  LA+LETLD GKP+ +S ++DVP  A+       W+     + 
Sbjct: 92  RARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQESEF 151

Query: 139 YDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPL 198
            D V              PVGVVG IVPWNFPL+M  WK+ PAL+ GN+VVLKP+E + L
Sbjct: 152 PDHV--------------PVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSL 197

Query: 199 TALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGE 258
           TAL  A LA +AG+P GVLN++ G G T G A+  H  +  + FTGST++ + +   +  
Sbjct: 198 TALLFAELAQQAGLPAGVLNIVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQTAG 256

Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTF 318
           S  K + LE GGKSP IVF DA D+ AA E    AI FNQG+VC AGSRLLV+  I D F
Sbjct: 257 SG-KSLTLELGGKSPFIVFEDA-DIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLF 314

Query: 319 LPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEET 378
           +  +   ++  K G PLD  +++GAL+   Q+  V S +E G  +GA+      +++ +T
Sbjct: 315 IARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQC----HQVVLDT 370

Query: 379 --GGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTK 436
             GG +  PT+  GV  A  +A EEIFGPVL  ++F T ++A+++AN++ YGLAA++W++
Sbjct: 371 PPGGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSE 430

Query: 437 DISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRD 478
            I  A   A  L+AG VW+N  +  D    FGG ++SG GR+
Sbjct: 431 TIGLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGRE 472



 Score = 76.6 bits (187), Expect = 3e-18
 Identities = 62/236 (26%), Positives = 100/236 (42%), Gaps = 5/236 (2%)

Query: 34  GETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRKATMIRFAGL 93
           GE         G  L  +   +  D + AV    A   +G W+  +P +R   +   A  
Sbjct: 531 GEVSMACHSTQGERLEDVGLGNRKDIRNAVA---AAVKAGGWTSASPHRRAQGLYYIAEN 587

Query: 94  LKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGLV 153
           L    EE A       G   +D    +V  + + L   G   DK    V   P   + L 
Sbjct: 588 LSARTEEFARRIASTTGVT-ADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALA 646

Query: 154 TREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIAALAIEAGIP 213
             E +GVVG + P   PL+     + P ++ GN VV+ PSE++PL A  +  +   + +P
Sbjct: 647 MPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLP 706

Query: 214 KGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAG 269
            GV+N++ G    +   LA H +V+ L   G  + +      S   N+KR +++ G
Sbjct: 707 AGVINIVTGKSAELLPVLAEHDEVEALWVRGPAEFSATAERLS-TGNLKRCFVDHG 761


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: 978
Number of extensions: 49
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: 793
Length adjustment: 38
Effective length of query: 459
Effective length of database: 755
Effective search space:   346545
Effective search space used:   346545
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