GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Klebsiella michiganensis M5al

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03865 BWI76_RS03865
           5-carboxymethyl-2-hydroxymuconate semialdehyde
           dehydrogenase
          Length = 488

 Score =  395 bits (1015), Expect = e-114
 Identities = 198/476 (41%), Positives = 302/476 (63%), Gaps = 3/476 (0%)

Query: 10  LENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQER 69
           + ++I+GK +  S Y  + +P+TGEV   V + G DE+  AV AA+EAFP W++   +ER
Sbjct: 4   INHWINGKNVAGSDYFHTTNPATGEVLAEVASGGADEVNQAVAAAKEAFPKWANLPMKER 63

Query: 70  SRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT 129
           +R++ ++ DL++Q++ E A  E+ D G  +   + + IPR+  NF FFA        +  
Sbjct: 64  ARLMRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGKTY 123

Query: 130 QMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWM 189
            +D    ++YT+  PVGV  L+SPWN+P    TWK+AP +A GNT + K SEL+ +TA  
Sbjct: 124 PVDDK-MLNYTLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTADR 182

Query: 190 LCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249
           L +L  +AG+P GV+N+V G G   G+ALV H +V  +SFTG   T   I + +    KK
Sbjct: 183 LGELALEAGIPAGVLNVVQGYGATAGDALVRHHDVRAVSFTGGTATGRNIMKNAG--LKK 240

Query: 250 LSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVE 309
            S+ELGGK+P +IFEDA+++  + A + + F+  GE C   SRIF+Q+SIY EF+KRF E
Sbjct: 241 YSMELGGKSPVLIFEDADIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKRFAE 300

Query: 310 ATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQA 369
              + +VG P+DP   +GALIS+ H EKV  Y++  + EGA +  G       LPA  + 
Sbjct: 301 RANRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAHLRN 360

Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429
           G F+ PTV+ D+ +      EEIFGPV C++PF  E E +  AN+V+YGLA+ +W+ +V 
Sbjct: 361 GNFLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQDVS 420

Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485
           +V R+A+ +++G+V+ N   +R+L  PFGG+K+SG GREG + S++ F E+K + +
Sbjct: 421 KVLRLARGIEAGMVFVNTQNVRDLRQPFGGVKASGTGREGGEYSFEVFAEMKNVCI 476


Lambda     K      H
   0.319    0.133    0.404 

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: 613
Number of extensions: 22
Number of successful extensions: 3
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: 487
Length of database: 488
Length adjustment: 34
Effective length of query: 453
Effective length of database: 454
Effective search space:   205662
Effective search space used:   205662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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