GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1647
          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 (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