GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_000009985.1:WP_011382978.1
          Length = 553

 Score =  164 bits (415), Expect = 5e-45
 Identities = 117/324 (36%), Positives = 166/324 (51%), Gaps = 31/324 (9%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           L++ G+ K +G       VLR +D+ +  GEF+ ++G SG GK+TL++++AGL +P  GE
Sbjct: 4   LELKGVAKSYGASS----VLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGE 59

Query: 65  IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALE--MRKMPKPERQKRIDEV 122
           + + GK V G P  DR +  VFQSY+L P L+V  NI  A++  M    K ER+ R+ + 
Sbjct: 60  VLLRGKPVDG-PGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKY 116

Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182
             M+ +SH  +RRPS+LSGG RQRVA+ RALA  P + L DEPLS LDA  R +++ EI+
Sbjct: 117 IGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIE 176

Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242
            + +    T + +T+D  EA+ L  RI  +  G     G P    N P     A     P
Sbjct: 177 AIWEQEKKTVILITNDVDEALLLADRIIPLNPGPGATFG-PSFKVNLPRPRDRAAVNSDP 235

Query: 243 TMNLLRGAVT----------GGQFGIQGAALNLAP-----PPSSANEVLLGVRPEHLVMQ 287
               LR  VT          GG+ G      N+AP     PP +  E      P+  V  
Sbjct: 236 DFKRLRAEVTEYLMAVGVERGGESGETRILPNVAPISFGGPPKAYREAGQVNNPDRYVE- 294

Query: 288 ETAPWRGRVSVVEPTGPDTYVMVD 311
                  RV  + PT      +VD
Sbjct: 295 -----FSRVKKIYPTPKGPLTVVD 313



 Score =  123 bits (308), Expect = 1e-32
 Identities = 71/220 (32%), Positives = 123/220 (55%), Gaps = 7/220 (3%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           ++ + + K +      + V+   D+ +  GEF+ L+G SGCGKST+L + AGL + +EG 
Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352

Query: 65  IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAA 124
           + + G+ V    P   D A+VFQ+ +L+P L+   N+   ++ R  P     +R+D V+ 
Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408

Query: 125 MLQ---ISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEI 181
            L+   +   +D++ S +S G RQRV + RA A  P+L L DEP   LD+  R E++  +
Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468

Query: 182 KRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLG 221
             +   + +T++ VTHD  EA+ L  ++ +M  G   ++G
Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIG 508


Lambda     K      H
   0.318    0.135    0.388 

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: 458
Number of extensions: 21
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: 355
Length of database: 553
Length adjustment: 32
Effective length of query: 323
Effective length of database: 521
Effective search space:   168283
Effective search space used:   168283
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:

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