GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Sinorhizobium fredii NGR234

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_000018545.1:WP_015887278.1
          Length = 360

 Score =  363 bits (931), Expect = e-105
 Identities = 198/369 (53%), Positives = 255/369 (69%), Gaps = 10/369 (2%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           M+ LE+RN+ K YG    +TLK+I++ ++ GEFL+L+G SGCGKSTL+N IAGL   SGG
Sbjct: 1   MSALEIRNIRKRYGD--VETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            IL+ +  I G  PKDRDIAMVFQSYALYP MSV  NI FGL++RK+P AE ++ V   +
Sbjct: 59  DILIGERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTA 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           +LLQIE+LL RKP QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K 
Sbjct: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKR 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           +HQ LKTT VYVTHDQIEAMTL  ++AVM+DG I+Q GTP +IY+ PA L+VA F+GSPP
Sbjct: 179 LHQMLKTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPP 238

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPL-GMQDAGLEDREVILGIRPEQIILANGEAN 299
           MN +        G  L +L S      LPL G    G   R V +GIRPE + LA  +A 
Sbjct: 239 MNILD---AEGTGSGLRILGSENT---LPLGGAFPNGTTGRRVKVGIRPEALRLAGDDAT 292

Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359
           G   + A V+V E TGP+ ++   + + ++   L P  +   G T    FD A + LFD 
Sbjct: 293 G-GRLTAIVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDP 351

Query: 360 KTGERLGVA 368
           ++G  L +A
Sbjct: 352 ESGLSLRMA 360


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: 406
Number of extensions: 13
Number of successful extensions: 4
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: 360
Length adjustment: 30
Effective length of query: 356
Effective length of database: 330
Effective search space:   117480
Effective search space used:   117480
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 Apr 09 2024. 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