GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Shewanella loihica PV-4

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__PV4:5210745 Shew_3173 succinic semialdehyde
           dehydrogenase (RefSeq)
          Length = 485

 Score =  295 bits (755), Expect = 2e-84
 Identities = 176/472 (37%), Positives = 267/472 (56%), Gaps = 11/472 (2%)

Query: 22  AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81
           ++I+G +T  V  + F+ ++P     +A+V    L D   A+  A+       WS+ +  
Sbjct: 14  SYIDGRWT--VGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPE--WSKRSAN 69

Query: 82  KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141
           +R A + ++ +L+ ++ E+L  L TL+ GKP+ ++   +I   A  I W AE   +VY +
Sbjct: 70  ERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKG-EIAYGAAFIDWFAEEGKRVYGD 128

Query: 142 VAPTP-HDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
             P P +D+  LV ++PVGVV +I PWNFP  M   K   ALA G + V +PS  +PL+A
Sbjct: 129 TIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSA 188

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHT-VGKALALHMDVDTLVFTGSTKIAKQLMVYAGES 259
           + +A+LA  AGIPAGV N++ G     +GK L  H DV    FTGST + K L+     S
Sbjct: 189 LAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATS 248

Query: 260 NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFL 319
            +K++ +E GG +P IVF DA D+ AA + A  +   N G+ C   +R+ V++ +   F 
Sbjct: 249 -VKKVSMELGGNAPFIVFDDA-DIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFT 306

Query: 320 PMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG 379
                A+   K G+ L    TVG ++    +  VL  ++     GAKL+ GG+ +  E G
Sbjct: 307 EKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPS--ELG 364

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
            +++ P I   VTN M +A+ EIFGPV  +I+FD+  EA+A+ANDT YGLAA  +  DI 
Sbjct: 365 ESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIG 424

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           +  + A  +  G V VN+    +  APFGG KQSGNGR+ S + L+ Y E+K
Sbjct: 425 RIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIK 476


Lambda     K      H
   0.316    0.132    0.390 

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: 541
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 497
Length of database: 485
Length adjustment: 34
Effective length of query: 463
Effective length of database: 451
Effective search space:   208813
Effective search space used:   208813
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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