GapMind for catabolism of small carbon sources

 

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

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>FitnessBrowser__ANA3:7023120
          Length = 619

 Score =  210 bits (535), Expect = 1e-58
 Identities = 176/579 (30%), Positives = 268/579 (46%), Gaps = 81/579 (13%)

Query: 44  GRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAAL-- 101
           G+PII IA + +   P + H  ++   V   I +AGGI  EF    + +        +  
Sbjct: 33  GKPIIAIANSFTQFVPGHVHLKDMGSLVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 92

Query: 102 ---DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGH 158
               R L    +  +++ +  D +V  + CDK TP  LMAA   ++P + +SGGPM  G 
Sbjct: 93  SLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGK 152

Query: 159 HK--GELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEA 216
            K   +LI    V   A    A   +  E   ++  +A P+ G C+ M TA SMN L EA
Sbjct: 153 TKLSDKLIKLDLV--DAMVAAADSSVSDEDSAKIERSACPTCGSCSGMFTANSMNCLTEA 210

Query: 217 LGMSLPGCASIPAPYRERGQMAYATGKRICELVLQ-------DIRPSQIMTRQAFENAIA 269
           LG+SLPG  S+ A + +R ++    G+R+  L  +          P  I + +AFENA+A
Sbjct: 211 LGLSLPGNGSMLATHADRRELFLEAGRRVMALTKRYYEQDDASALPRNIASFKAFENAMA 270

Query: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPA-GKYLGEGFHRAG 328
           +  A+G SSN   HL+A A+   V  ++DD  R+   VP L    P+  KY  E  HRAG
Sbjct: 271 LDIAMGGSSNTVLHLLAAAQEADVAFTMDDIDRMSRQVPHLCKVAPSTAKYHMEDVHRAG 330

Query: 329 GVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLK---------- 378
           GV  ++ EL +AG LH D   V+    G +   S+ +  DV+   D  +K          
Sbjct: 331 GVMGILGELDRAGLLHTDVPHVAADAGGNL--KSVLAKYDVMQTQDDKVKQFFMAGPAGI 388

Query: 379 --------------------------------HRAGFIVLSGNFFDS-AIMKMSVVGEAF 405
                                              G  VLSGN  D+  I+K + V E  
Sbjct: 389 PTTKAFSQDCRWPSLDDDRREGCIRSREFAFSQEGGLAVLSGNLADNGCIVKTAGVDE-- 446

Query: 406 RKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEV 465
                    +  +F   A V+E  +D  A I    +   +  ++VIR  G  G PG  E+
Sbjct: 447 ---------SNLTFIGSARVYESQDDAVAGILGGEVVAGD--VVVIRYEGPKGGPGMQEM 495

Query: 466 VNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVD 524
             + P + L  +G+  +   + DGR SG ++  SI ++SPEAA GG +AL++  DR+++D
Sbjct: 496 --LYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGTIALIENGDRIEID 553

Query: 525 LNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQ 563
           +  R++ L + D E+A RR       P +   W+ L RQ
Sbjct: 554 IPKRSIKLAVSDAELAARRETMLARGPMA---WKPLSRQ 589


Lambda     K      H
   0.319    0.135    0.407 

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: 827
Number of extensions: 42
Number of successful extensions: 6
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: 594
Length of database: 619
Length adjustment: 37
Effective length of query: 557
Effective length of database: 582
Effective search space:   324174
Effective search space used:   324174
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.

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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