GapMind for catabolism of small carbon sources

 

Aligments for a candidate for QDPR in Sinorhizobium meliloti 1021

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate SMa1191 SMa1191 nitric oxide dioxygenase

Query= CharProtDB::CH_003330
         (396 letters)



>FitnessBrowser__Smeli:SMa1191
          Length = 403

 Score =  342 bits (876), Expect = 1e-98
 Identities = 178/399 (44%), Positives = 250/399 (62%), Gaps = 8/399 (2%)

Query: 1   MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60
           ML  +T   VKAT P+L + G  +  HFY RMF  +PELK IFNM++Q  G+Q++AL  A
Sbjct: 1   MLTQKTKDIVKATAPVLAQHGYAIIQHFYKRMFQAHPELKNIFNMAHQERGEQQQALARA 60

Query: 61  IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118
           + AYA+NIEN  +L   ++ IA KH S  ++PEQY IVGEHLLA++ E+       E++ 
Sbjct: 61  VYAYAANIENPESLSAVLKDIAHKHASLGVRPEQYPIVGEHLLASIKEVLGDAATDEIIS 120

Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178
           AW +AYG LA++    E+E+Y  +  +AGGW G R F +  K P S +ITSF LEP DGG
Sbjct: 121 AWAQAYGNLADILAGMESELYERSEERAGGWAGWRRFIVREKNPESDVITSFVLEPADGG 180

Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG-----GQVSNWL 233
            VA++ PGQY  V ++     +Q+IRQYSL+  P+G+ YRI+VKRE+G     G VS+ L
Sbjct: 181 PVADFEPGQYTSVAVQVPKLGYQQIRQYSLSDSPNGRSYRISVKREDGGLGTPGYVSSLL 240

Query: 234 HNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWF 293
           H+  NVGD +KL AP G+F++ V+  TP+ LIS GVG TPM++ML   A      +V + 
Sbjct: 241 HDEINVGDELKLAAPYGNFYIDVSATTPIVLISGGVGLTPMVSMLKK-ALQTPPRKVVFV 299

Query: 294 HAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFS 353
           H A N  VHA  D +KE  ++ P F    +Y +P   D     +D  GL+D+ K++ +  
Sbjct: 300 HGARNSAVHAMRDRLKEASRTYPDFKLFIFYDEPLPTDIEGRDYDFAGLVDVEKVKDSIL 359

Query: 354 DPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392
                +Y+CGPV FM+    +L+ LG+ +  IHYE FGP
Sbjct: 360 LDDADYYICGPVPFMRMQHDKLLGLGITEARIHYEVFGP 398


Lambda     K      H
   0.318    0.135    0.404 

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: 410
Number of extensions: 17
Number of successful extensions: 4
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: 396
Length of database: 403
Length adjustment: 31
Effective length of query: 365
Effective length of database: 372
Effective search space:   135780
Effective search space used:   135780
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: 50 (23.9 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 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