GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagPcb in Sphingomonas koreensis DSMZ 15582

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component

Query= SwissProt::O34521
         (452 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1647 Ga0059261_1647 PTS system,
           N-acetylglucosamine-specific IIBC component
          Length = 560

 Score =  440 bits (1132), Expect = e-128
 Identities = 219/476 (46%), Positives = 307/476 (64%), Gaps = 25/476 (5%)

Query: 1   MLSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAI 60
           +L  LQ LG++ MLPIAVLP  G++L +G+ D+ +I FV  AGTA+F +L ++FAIG+A+
Sbjct: 4   ILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGVAV 63

Query: 61  GISKDSNGAAGLSGAISYLML-------------------DAATKTIDKT------NNMA 95
           G ++D NGAA L+G   YL+                    DAA K + +       + + 
Sbjct: 64  GFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQAWATGQIDRLE 123

Query: 96  VFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQS 155
           V  GII+GLI G  YNRF    LPEYL FF GRR VPI   I  ++LAG+ G  +  I S
Sbjct: 124 VPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAHISS 183

Query: 156 CINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTGDLARFFAK 215
            +++    ++  GG G  ++G+ NRLL+  GLHH+LNN+ WF  G++ G TGDL RFFA 
Sbjct: 184 ALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDFGGATGDLGRFFAG 243

Query: 216 DPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEF 275
           DP AG +M+GFFP+MMFGLPAACLAM   A+P +RKA  GM+   A T+F+TG+TEPIEF
Sbjct: 244 DPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIEF 303

Query: 276 AFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGI 335
            FMFL+P+LYA+HAVLTG+++ +++ LGI+ GF FSAG  DYVL++ ++ +P +LL VG 
Sbjct: 304 TFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKLSTRPWMLLPVGA 363

Query: 336 CYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTID 395
            YA +Y+ +F   I+ L+L TPGRE  +      E    +      +K LGG  NL ++D
Sbjct: 364 AYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFVKALGGAANLTSVD 423

Query: 396 HCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451
            C TRLRL V D + VD+A L   GA+G+++    + QV++GP  +  AEE+R A+
Sbjct: 424 ACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADLVAEEIRGAI 479



 Score = 29.6 bits (65), Expect = 3e-04
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 381 MLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVV 425
           +L  LGG+ N++ +     R R+ V D A  DEA L  A A G V
Sbjct: 505 ILAALGGEANIRALQALHGRFRVEVVDAARTDEASL-LAAANGAV 548


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: 691
Number of extensions: 41
Number of successful extensions: 3
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: 452
Length of database: 560
Length adjustment: 34
Effective length of query: 418
Effective length of database: 526
Effective search space:   219868
Effective search space used:   219868
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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