GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5210745
          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:

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