GapMind for catabolism of small carbon sources

 

Alignments 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.

Links

Downloads

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:

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