GapMind for catabolism of small carbon sources

 

Aligments for a candidate for antA in Marinobacter adhaerens HP15

Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate GFF1128 HP15_1106 Rieske (2Fe-2S) domain protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740
         (461 letters)



>lcl|FitnessBrowser__Marino:GFF1128 HP15_1106 Rieske (2Fe-2S) domain
           protein
          Length = 414

 Score =  375 bits (964), Expect = e-108
 Identities = 194/420 (46%), Positives = 267/420 (63%), Gaps = 15/420 (3%)

Query: 44  MELIFEKNWIYACHESEIANPNDFLTMRAGRQPMIITRDGNNQLHALINACQHRGATLTR 103
           M+ IFE NW+Y  HES+I   NDF T   GR P+IITRD +  L+A +N C HRGA L R
Sbjct: 1   MKYIFEGNWVYLAHESQIQENNDFFTTYIGRHPIIITRDKSGNLNAFLNICTHRGAMLCR 60

Query: 104 VSKGNQSTFTCPFHAWCYKSDGRLVKVKAP--GEYPEGFD-KATRGLKK-ARIESYKGFV 159
             KGN+S  TCPFH W + + G+LVKVK      YP+ F+ +    LK  A+ +SY+GF+
Sbjct: 61  SKKGNKSVMTCPFHGWSFNNSGKLVKVKDEKGSGYPDSFNCEGELNLKNIAKFDSYRGFL 120

Query: 160 FISLDVNGSDSLEDYLGDAKVFFDMMVAQSPTGELEILPGKSTYSYDGNWKLQHENGLDG 219
           F SL+ +  D L DYLGD     DM+V QS   E+E+L G STY++DGNWK+Q ENG+DG
Sbjct: 121 FGSLNSDVQD-LNDYLGDTTKIIDMIVDQSED-EIEVLRGASTYTFDGNWKVQAENGVDG 178

Query: 220 YHVSTVHYNYVSTVQHRQQVNAANGGVS-DTLDYSKLGAGDAETDDGWFSFKNGHSLLFS 278
           YHVS VH+NYV+TV  R+Q  + +   S D   ++K   G        ++FKNGH+LL+ 
Sbjct: 179 YHVSAVHWNYVATVARRKQGLSEDSAKSVDLSSWNKQKGGS-------YAFKNGHTLLWM 231

Query: 279 DMPNPTVRAGYATVMPRLIEEYGQQQAEWMMHRLRNLNIYPSLFFMDQISSQLRIVRPVA 338
           + PNP  R   A     L  +YG+ +A+WM+  +RNL IYP++F MDQ S+Q+R  RP++
Sbjct: 232 EAPNPQDRP-LAEKREELSRKYGKNRADWMISNIRNLGIYPNVFLMDQTSTQIRHFRPIS 290

Query: 339 WNKTEITSQCIGVKGESDADRENRIRQFEDFFNVSGMGTPDDLVEFREAQRGFQARLERW 398
            NKTE+T  C   K ES   R  RIRQ+EDFFN +GM TPDDL +F  +Q  F A    W
Sbjct: 291 VNKTEVTIYCFAPKNESGEARNRRIRQYEDFFNATGMATPDDLEQFNSSQISFHASKAPW 350

Query: 399 NEVSRGSEKWVEGPTPNSEVLGINPVLTGTEFTHEGLYINQHGSWQRFLLQGLEQKALKL 458
           N++SRG++ W++G    +E + I P+L+G +   EGL++ QH  W   LL+G+  +  K+
Sbjct: 351 NDLSRGAKHWIDGQDKEAESIDIFPLLSGVKSEDEGLFVMQHECWANALLRGMSDEEDKV 410


Lambda     K      H
   0.318    0.135    0.415 

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: 560
Number of extensions: 22
Number of successful extensions: 6
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: 461
Length of database: 414
Length adjustment: 32
Effective length of query: 429
Effective length of database: 382
Effective search space:   163878
Effective search space used:   163878
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 (21.7 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 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