GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1897 in Klebsiella michiganensis M5al

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS23390 BWI76_RS23390
           oligogalacturonide ABC transporter ATP-binding protein
          Length = 375

 Score =  299 bits (765), Expect = 1e-85
 Identities = 163/377 (43%), Positives = 239/377 (63%), Gaps = 12/377 (3%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA +    + K Y  G    +  I+LKI DGEF+++VGPSGC KST +  +AGLETISGG
Sbjct: 1   MAEVIFNKLEKVYSNGFK-AVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGG 59

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            + + +  ++ ++PK R IAMVFQ+YALYP M+VR+N+AFGLK+ K+P  +I+ +V   +
Sbjct: 60  EVRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAA 119

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           K+L++E LL R P QLSGGQ QRVA+GRA+ ++P ++LFDEPLSNLDAKLR  MR  +  
Sbjct: 120 KILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISD 179

Query: 181 MHQRLK-----TTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235
           +H++LK      TTVYVTHDQ EAMT+GD++ VMK G I Q  TP ++Y+ P N+FVA F
Sbjct: 180 LHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHKPKNMFVAGF 239

Query: 236 IGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILAN 295
           IG+P MN  P +L  + GRL   +  G       L  +    ++++V  G+RPE + +++
Sbjct: 240 IGAPEMNIRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQQVFFGVRPEFVSISD 299

Query: 296 GEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGE-----TLTLQFD 350
            E     +   E+   E  G +  V++ + D ++  R+  D A  + E      +  +FD
Sbjct: 300 -EPFAEGSCTGEMVRVENMGHEFFVYLKVADYELTARVPSDEAKPMIEKGLHRKVHFKFD 358

Query: 351 PAKVLLFDAKTGERLGV 367
             K  +FDAKT + + +
Sbjct: 359 LNKCHIFDAKTEQNISL 375


Lambda     K      H
   0.319    0.138    0.393 

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: 392
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 386
Length of database: 375
Length adjustment: 30
Effective length of query: 356
Effective length of database: 345
Effective search space:   122820
Effective search space used:   122820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 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