GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Shewanella sp. ANA-3

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_609
         (578 letters)



>FitnessBrowser__ANA3:7023120
          Length = 619

 Score =  230 bits (586), Expect = 1e-64
 Identities = 180/577 (31%), Positives = 280/577 (48%), Gaps = 59/577 (10%)

Query: 6   PSLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAE 65
           P LRSA    T  +N    R+  +  G+ D+ F GKPII I N++++  P + H + +  
Sbjct: 2   PKLRSAT--STEGRNMAGARALWRATGVKDNDF-GKPIIAIANSFTQFVPGHVHLKDMGS 58

Query: 66  HVKRGVIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEEAIRGNPIDGVVL 120
            V   + EAGG   EF   +  +   +    ML    +R L +  VE  +  +  D +V 
Sbjct: 59  LVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVC 118

Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITI 180
           ++ CDK TP +LM A   ++P + V+GGPM  GK K  D      +          +++ 
Sbjct: 119 ISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADSSVSD 178

Query: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240
           +D    E     + G+C+ M TA++M C+ EALG SLP N ++ A  A R  L   +G R
Sbjct: 179 EDSAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRR 238

Query: 241 AVEMVREDLKLS-------KILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQLDL 293
            + + +   +          I + +AFENA+ ++ A+GGS+N V+HL A A    V   +
Sbjct: 239 VMALTKRYYEQDDASALPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEADVAFTM 298

Query: 294 DDWTRIGRGMPTIVDLQPS-GRFLMEEFYYAGGLPAVLRRLGEANL----IPH------P 342
           DD  R+ R +P +  + PS  ++ ME+ + AGG+  +L  L  A L    +PH       
Sbjct: 299 DDIDRMSRQVPHLCKVAPSTAKYHMEDVHRAGGVMGILGELDRAGLLHTDVPHVAADAGG 358

Query: 343 NALTVSGKSIGENTKDAPI----------------YGQD------------EVIRTLDNP 374
           N  +V  K     T+D  +                + QD              IR+ +  
Sbjct: 359 NLKSVLAKYDVMQTQDDKVKQFFMAGPAGIPTTKAFSQDCRWPSLDDDRREGCIRSREFA 418

Query: 375 IRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVDAS 434
              +GG+ VL GNLA  G ++K +      +   G A V+E+ D+  A I   E  V A 
Sbjct: 419 FSQEGGLAVLSGNLADNGCIVKTAGVDESNLTFIGSARVYESQDDAVAGILGGE--VVAG 476

Query: 435 SILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGV-TDMVRISDARMSGTAYGTVVLHVAPE 493
            ++V++  GPKG PGM E+  +   + L ++G+      I+D R SG   G  + HV+PE
Sbjct: 477 DVVVIRYEGPKGGPGMQEM--LYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPE 534

Query: 494 AAAGGPLAAVKEGDWIELDCTSGRLHLDIPDAELAAR 530
           AAAGG +A ++ GD IE+D     + L + DAELAAR
Sbjct: 535 AAAGGTIALIENGDRIEIDIPKRSIKLAVSDAELAAR 571


Lambda     K      H
   0.319    0.136    0.409 

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: 807
Number of extensions: 43
Number of successful extensions: 8
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: 578
Length of database: 619
Length adjustment: 37
Effective length of query: 541
Effective length of database: 582
Effective search space:   314862
Effective search space used:   314862
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: 53 (25.0 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