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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__ANA3:7023120 Shewana3_0358 dihydroxy-acid
           dehydratase (RefSeq)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources