GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Magnetospirillum magneticum AMB-1

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000009985.1:WP_011382978.1
          Length = 553

 Score =  129 bits (323), Expect = 2e-34
 Identities = 79/213 (37%), Positives = 124/213 (58%), Gaps = 7/213 (3%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           ++ELK V K YG   VL++I+L +++GE + I+G SGSGK+T +  M GL +  +GEV++
Sbjct: 3   ILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLL 62

Query: 61  NNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLA-PMKLQKKSKKEAEETAFKY 119
               ++             +VFQ ++L P +TV  N+ LA    +   SK E +    KY
Sbjct: 63  RGKPVDGPGADR------GVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKY 116

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           + +VGL   A   P+ LSGG +QRVA+AR+L      +L DEP SALD  T  ++ D ++
Sbjct: 117 IGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIE 176

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDG 212
            I  Q   T++++T+++  A  +ADRII +  G
Sbjct: 177 AIWEQEKKTVILITNDVDEALLLADRIIPLNPG 209



 Score =  105 bits (263), Expect = 1e-27
 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 22/244 (9%)

Query: 2   IELKNVNKYYGTHH----VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGE 57
           +E   V K Y T      V+   +L + +GE + +IG SG GKST +    GL +VS G 
Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352

Query: 58  VVVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKK-SKKEAEETA 116
           V+++   ++            A+VFQ  +L+P +T LQN+ L   ++    S  E  +  
Sbjct: 353 VILDGREVSEAGPDR------AVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIV 406

Query: 117 FKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLD 176
             YL+ VGL D  +   + +S G +QRV IAR+       +L DEP   LD  T  E+ +
Sbjct: 407 SYYLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQE 466

Query: 177 VMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMED------GAIVEENIPSEFFSNPKTE 230
           V+ E+  ++  T + VTH++  A  +AD+++ M +      G ++  +IP      P+T 
Sbjct: 467 VLMEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIGKVLNVDIP-----RPRTR 521

Query: 231 RARL 234
           RA L
Sbjct: 522 RALL 525


Lambda     K      H
   0.317    0.133    0.372 

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: 252
Number of extensions: 13
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: 242
Length of database: 553
Length adjustment: 29
Effective length of query: 213
Effective length of database: 524
Effective search space:   111612
Effective search space used:   111612
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: 49 (23.5 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