Aligments for a candidate for xacD in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for xacD in Shewanella amazonensis SB2B

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)

Query= reanno::HerbieS:HSERO_RS05205
         (585 letters)



>FitnessBrowser__SB2B:6939185
          Length = 618

 Score =  218 bits (555), Expect = 6e-61
 Identities = 178/584 (30%), Positives = 278/584 (47%), Gaps = 73/584 (12%)

Query: 12  LRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPCNAHFRKIAEHV 71
           LRSA    T  +N    R+  +  G+ D +F GKP+I I N++++  P + H + +   V
Sbjct: 4   LRSAT--STEGRNMAGARALWRATGVKDTDF-GKPIIAIANSFTQFVPGHVHLKDMGSLV 60

Query: 72  RRGIIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEESIRGNPIDAVVLLT 126
              I EAGG   EF   +  +   +    ML    +R L +  VE  +  +  DA+V ++
Sbjct: 61  ASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120

Query: 127 GCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAG---EIT 183
            CDK TP +LM A   ++P + V+GGPM  GK +   +    +   L + + A     I+
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTK---LSDKLIKLDLVDAMVAAADDRIS 177

Query: 184 IHDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGM 243
             D    E     + G+C+ M TA++M C+ E+LG+SLP N ++ A  A R  L   +G 
Sbjct: 178 DADSEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGR 237

Query: 244 RIVDMV--WEGLTLSKILTR-----KAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLE 296
           R++ +   + G   + +L R     KAFENA+  + A+GGS+N V+HL A A    VD  
Sbjct: 238 RVMKLAKRYYGDDDASVLPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFT 297

Query: 297 LEDWTRIGRGTPTIVDLQPS-GRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQ- 354
           ++D  RI R  P +  + PS  +Y ME+ + AGG+ A+L  L  A LL H D   V  + 
Sbjct: 298 MDDIDRISRKVPHLCKVAPSTPKYHMEDVHRAGGVMAILGELDRAGLL-HTDVNHVASED 356

Query: 355 ----------------------------------------TMWDNVKDAPIYNDEVVRPL 374
                                                     WD + D     +  +R  
Sbjct: 357 GTLKSVLERFDVVLTKDEKVHEFFRAGPAGIPTTRAFSQSCRWDTLDDD--RREGCIRSR 414

Query: 375 AKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDFNHYKERINDPDLDV 434
                ++GG+ +L GNLA  G ++K +      +K  G A V+E        I     +V
Sbjct: 415 EFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGG--EV 472

Query: 435 DASCVLVMKNVGPKGYPGMAEV--GNMGLPPKVLATGVKDMVRISDARMSGTAYGTVILH 492
            A  V+V++  GPKG PGM E+      L  + L T       I+D R SG   G  I H
Sbjct: 473 VAGDVVVIRFEGPKGGPGMQEMLYPTSYLKSRGLGT---QCALITDGRFSGGTSGLSIGH 529

Query: 493 VAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEA 536
           V+PEAA+GG +G++++GD I++D     ++L +S+ E++ R  A
Sbjct: 530 VSPEAASGGTIGLIENGDRIDIDIPGRSIKLLVSDAELESRRAA 573


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: 883
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: 585
Length of database: 618
Length adjustment: 37
Effective length of query: 548
Effective length of database: 581
Effective search space:   318388
Effective search space used:   318388
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 paper from 2022 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