Alignments for a candidate for treEIIA in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Maridesulfovibrio zosterae DSM 11974

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_027722339.1 H589_RS0112545 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>NCBI__GCF_000425265.1:WP_027722339.1
          Length = 829

 Score =  432 bits (1110), Expect = e-125
 Identities = 266/669 (39%), Positives = 380/669 (56%), Gaps = 26/669 (3%)

Query: 178 NPNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGED 237
           N  GLHARPAA     A  F +S+ + K  DSA+AKS+  +  L   +GD + +S  G D
Sbjct: 168 NKMGLHARPAANLVSTAGKFKSSVAIRKGADSASAKSINQVALLSVKNGDTITISVSGAD 227

Query: 238 AELAISTLAQLLADGCGEAVTPVAV----VAPVVEAQEVSTKLLRGVCASAGSAFG--YV 291
           A+ A   L +L  D  GE    VA     + PVV+A + +   + G   S G A G  YV
Sbjct: 228 AQEAFDALIKLHKDNFGERDEDVAELVEDIKPVVQAGDGT---IVGAPGSGGYAVGTAYV 284

Query: 292 VQVAERTLEMPEFAADQQLERESLERALMHAT---QALQRLRDNAAGEAQADIFKAHQEL 348
            Q     +E    + D + E E L+ A+  A    + LQR  +  +G+A A IF+ H  +
Sbjct: 285 HQATLPEVERKNIS-DVETELEKLDLAISTALSDIKILQRETEKTSGKANAAIFEVHAMI 343

Query: 349 LEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLK 407
           + D  + ++A  +++E + +A +AW          +++L  T +  RA D+MD G RVL+
Sbjct: 344 ISDKDMRDKAAEIVSEQQINADYAWFEVMNKITADYRNLDDTYMQARAADVMDCGGRVLR 403

Query: 408 LILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLP 467
           ++ G  +    L + AI++A  L+PS  A LD  KVLG  T  GG TSH AIL+R++G+P
Sbjct: 404 ILAGEEEQGICLENGAIIVAHDLSPSDVAGLDLEKVLGVVTEIGGVTSHAAILSRSMGIP 463

Query: 468 AVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARA 527
           AV G    +  + +GT + L+  +G +  +P  SV+  +  KR       +      A  
Sbjct: 464 AVIGAGKSIQQIQNGTIIALNGFEGVIWPEPEQSVVNDIAEKRVLWLAEREEAKAKGAAP 523

Query: 528 AVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAI 587
           A T DG    V  N+   A+  +    GAEG+GL R+EFL+Q RS AP+ DEQ   Y   
Sbjct: 524 AKTLDGTDIMVMGNIGVPADAPRVFEYGAEGVGLFRTEFLFQDRSQAPTEDEQFDAYVEA 583

Query: 588 ARALGPQRN-LVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAIL 646
           ARA+  Q N +++RTLD+GGDKP+ Y+    E NPFLG RGIR C+ RP+L R Q RA+L
Sbjct: 584 ARAM--QGNPVIIRTLDIGGDKPVKYLDTPEEDNPFLGERGIRFCMARPELFRTQLRALL 641

Query: 647 SSAGLARLHIMLPMVSQLSEL-------RLARLMLEEEALALGLRELPKLGIMIEVPAAA 699
            +A    + IM PM+S + EL         AR +L  E + +   E  K GIMIEVPAA 
Sbjct: 642 RAASEENIWIMYPMISDVDELSSVLEIQNQAREVLVSEGVKIA--EKIKTGIMIEVPAAV 699

Query: 700 LMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHG 759
            +AD  A + DFFSIGTNDLTQY +A DR +  ++   D+ +P+VLR++A T  AA   G
Sbjct: 700 AVADKLAQKCDFFSIGTNDLTQYVMAADRGNASVSKLCDNLNPAVLRMVAMTCDAAKKAG 759

Query: 760 KWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLE 819
             VG+CG LA  + A  LLLGLG+DELS++ P IP +K AIR V + DC+A+A +VL   
Sbjct: 760 IEVGMCGELAGNSKASALLLGLGLDELSMNGPAIPEVKEAIRSVNMDDCRALAQKVLEAN 819

Query: 820 SAEQVREAL 828
           S+++VR+ L
Sbjct: 820 SSDEVRDLL 828


Lambda     K      H
   0.318    0.132    0.370 

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: 1305
Number of extensions: 52
Number of successful extensions: 5
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: 844
Length of database: 829
Length adjustment: 42
Effective length of query: 802
Effective length of database: 787
Effective search space:   631174
Effective search space used:   631174
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources