GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Catellicoccus marimammalium M35/04/3

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC

Query= SwissProt::O34521
         (452 letters)



>NCBI__GCF_000313915.1:WP_083848942.1
          Length = 553

 Score =  187 bits (474), Expect = 1e-51
 Identities = 152/543 (27%), Positives = 245/543 (45%), Gaps = 104/543 (19%)

Query: 4   FLQKLGKSFMLPIAVLPAVGIILALGR-------EDVFNIPFVYQ-AGTAVFDHLPLIFA 55
           F QK GK+ M+ IAV+PA G+++++G+            I  V +  G A+  +LP++FA
Sbjct: 9   FWQKFGKALMVVIAVMPAAGLMISIGKLIAMAQVSLAVTIGGVTENIGWAIIGNLPILFA 68

Query: 56  IGIAIGISKDSNGAAGLSGAISYLMLDAATKTIDKTN----------------------- 92
           + I    +K+  G A  SG +++++++  T  +                           
Sbjct: 69  LAIGGSWAKERAGGAFASG-LAFILINRITGAVFGVTKEMLANPEATVHTIFGQKILVNG 127

Query: 93  -----------NMAVFGGIIAGLIAGYTYNRFKD-TKLPEYLGFFSGRRLVPILTAIITI 140
                      NM VF GIIAG      YN++ +  KLP  L FF+G+R VP +  + ++
Sbjct: 128 YFTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGKRFVPFVVILWSV 187

Query: 141 ILAGIFGVVWPPIQSCINSFGEWMLGLGGI----GAGIFGLFNRLLIPLGLHHVLNNIFW 196
           I+A +  V WP  Q+ IN FG+W+   G         I+G   RLL+P GLHH+L     
Sbjct: 188 IIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLPFGLHHMLTIPMN 247

Query: 197 FQ--FGEYNGVTGDLA--RFFAKDPTAGTYMTGFFPIMMFG------------------- 233
           +    G Y+ +TG  A      +DP    ++T    +   G                   
Sbjct: 248 YTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQLLESIRPARFKV 307

Query: 234 ---------LPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLL 284
                    L     AM    +P ++K    + +  AL  F+TG+TEP+EF FMF    L
Sbjct: 308 GQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEPLEFMFMFAGIPL 367

Query: 285 YAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYV------LSYGIAEKPLLLLLVGICYA 338
           Y V+A+L G++  + + + +R     + G I+ +      +  G+    +  ++  I + 
Sbjct: 368 YVVYALLQGVAFGLADIIDLR---LHAFGNIELLTRLPMSIKAGLGMDIINFIITCIVFF 424

Query: 339 AVYFIVFYVLIKALNLKTPGR-----EDDDVDEVLDENTV------QDVNENIM--LKGL 385
            + + V   +IK  ++ TPGR     E +D     D  T        + N  +M  ++ L
Sbjct: 425 FLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTATSSTKPSEANNQVMNIIQLL 484

Query: 386 GGKENLQTIDHCATRLRLTVKDTALV-DEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAA 444
           GGKEN+  +D C TRLR+TVKDT  V DE   KK GA G++      VQ + GP  +   
Sbjct: 485 GGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGLIHK-NNGVQAVYGPKADVLK 543

Query: 445 EEL 447
            ++
Sbjct: 544 SDI 546


Lambda     K      H
   0.326    0.144    0.429 

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: 618
Number of extensions: 39
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 452
Length of database: 553
Length adjustment: 34
Effective length of query: 418
Effective length of database: 519
Effective search space:   216942
Effective search space used:   216942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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