GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Marivita geojedonensis DPG-138

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  320 bits (819), Expect = 5e-92
 Identities = 187/373 (50%), Positives = 238/373 (63%), Gaps = 34/373 (9%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           M+ V LE + K Y GQT+  +   +LD+QD EF VFVGPSGCGK+T LRM+AGLE+ TEG
Sbjct: 1   MSGVTLESVIKRY-GQTQ-VIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            + IG R V  + P DR ++MVFQ YALYPHMTV +NM FGLK+      +I  +V EA+
Sbjct: 59  TIRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEAS 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           +IL +   L RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV+MR EI +
Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+ +  T+IYVTHDQ EAMT+ D+IVV+R G I+Q   P  +Y  P N FVAGFIGSP+
Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPS 238

Query: 241 MNFIR-----GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHD 295
           MNFIR     GE+V DG        S+S            AS   G+ V++G+RPE L  
Sbjct: 239 MNFIRGRVQGGEVVSDG-----LVHSVS----------KTASAQEGQEVLIGLRPEHLE- 282

Query: 296 EEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPN--TIVARVNPRHVYHVGSSVKLAI 353
                   P S    +V++ E +G   Y H  IGP+   I+      H    G  V L +
Sbjct: 283 ------LRPGS--SHRVDLTESLGGVSYAHL-IGPDGEKIIVEERGDHRSSDGDMVDLVV 333

Query: 354 DLNKIHIFDAETE 366
           D + + +FDA+TE
Sbjct: 334 DPDHMFLFDAKTE 346


Lambda     K      H
   0.321    0.138    0.395 

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: 399
Number of extensions: 16
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: 384
Length of database: 350
Length adjustment: 30
Effective length of query: 354
Effective length of database: 320
Effective search space:   113280
Effective search space used:   113280
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 (21.8 bits)
S2: 49 (23.5 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