GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Synechococcus elongatus PCC 7942

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase

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



>FitnessBrowser__SynE:Synpcc7942_0489
          Length = 459

 Score =  146 bits (369), Expect = 1e-39
 Identities = 132/433 (30%), Positives = 206/433 (47%), Gaps = 26/433 (6%)

Query: 67  RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126
           +ATF+ G    LA   R A+L   A L+  N  EL      D+ KP  ++ + +I     
Sbjct: 17  QATFDRGDTRTLA--FRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRD 74

Query: 127 AIHWTAEAIDKVY--DEVAPTPHDQLGLVTR--EPVGVVGAIVPWNFPLLMACWKLGPAL 182
            I  T + + +    ++ + +   Q G   R  EP+GVV  I PWN+P  +    L  A+
Sbjct: 75  QIKLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAI 134

Query: 183 ATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVF 242
           A GN  VLKPSE +P T+  I +L  +   P   + VL G   +V +AL +    D + F
Sbjct: 135 AAGNCAVLKPSELAPATSSLIQRLISDRFDP-DYIRVLEG-DASVSQAL-ITQPFDHIFF 191

Query: 243 TGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVC 302
           TG T I +++M  A E N+  + LE GGKSP IV  D  DL  AA   A    FN G+ C
Sbjct: 192 TGGTAIGRKVMAAAAE-NLTPVTLELGGKSPCIVDTDI-DLDVAARRIAWGKFFNAGQTC 249

Query: 303 TAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDT--QQMNTVLSYIEAG 360
            A   LLV+R++ + F+  +++ ++ +   +P         + D   Q++N++L  ++  
Sbjct: 250 IAPDYLLVQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLL--VDGT 307

Query: 361 HKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVA 420
            + G ++         +    Y+ PT+   V     I QEEIFGP+L ++ +D  +EA+A
Sbjct: 308 IRHGGQV---------DRSDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIA 358

Query: 421 IANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQ--YDGGDMTAPFGGFKQSGNGRD 478
                P  LA  +++ D     +      AGSV +N      G   A FGG   SG G  
Sbjct: 359 QIRAQPKPLALYLFSRDRQVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGY 418

Query: 479 KSLHALEKYTELK 491
               + E ++  K
Sbjct: 419 HGKASFETFSHYK 431


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: 494
Number of extensions: 23
Number of successful extensions: 5
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: 459
Length adjustment: 34
Effective length of query: 463
Effective length of database: 425
Effective search space:   196775
Effective search space used:   196775
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: 51 (24.3 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