Alignments for a candidate for PS417_11890 in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Stutzerimonas stutzeri A1501

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_011914604.1 PST_RS17845 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>NCBI__GCF_000013785.1:WP_011914604.1
          Length = 525

 Score =  246 bits (628), Expect = 1e-69
 Identities = 167/490 (34%), Positives = 252/490 (51%), Gaps = 16/490 (3%)

Query: 28  LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87
           +++  VSK F G +ALS      R G V AL+GENGAGKS+LM I AG+Y P++G L + 
Sbjct: 7   IQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLIN 66

Query: 88  GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMI--DHREMHRCT 145
              V    P  A +  I M+HQ   L+   ++AENI +   +  G H     HR+     
Sbjct: 67  DNAVRLSGPRDASRYHIGMVHQHFKLVKPFTVAENIQLALPEGPGNHAFSGSHRQRLAAL 126

Query: 146 AQLLE----RLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVA 201
            Q +      L  ++DP +   +LS+AE+Q VEI K +   + ILI+DEPT+ +TD E  
Sbjct: 127 EQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAE 186

Query: 202 HLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 261
            L   +     QG  +I +THKM++V   AD V V R G  I      ++    L+ + V
Sbjct: 187 RLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRLTV 246

Query: 262 GRELSQLFPVREKPIGDLLMSVRDLRL-----DGVFKGVSFDLHAGEILGIAGLMGSGRT 316
           G E +     +    G++ + VRDLR       GV  GV+  L AGEI GIAG+ G+G++
Sbjct: 247 G-ESAPASEYQPAIPGEVRLQVRDLRSTGAGGQGVLNGVNLSLRAGEIYGIAGVGGNGQS 305

Query: 317 NVAEAIFGITPSDGGEICLDG-QPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 375
            +A  + G+     G + L G   +R +      E   A +  DR  + L   LSV EN 
Sbjct: 306 ELANVLMGLPEPCDGTLELTGFGDLRRASAEQRRELRIAAIPADRYGAALAGELSVAENF 365

Query: 376 EMAVL--PHYAGNGFIQQKALRALCEDMCKKLRVK-TPSLEQCIDTLSGGNQQKALLARW 432
            +  +    Y     +++K L A   +      V+   SL+Q    LSGGN QK ++AR 
Sbjct: 366 GVGQVHSGRYGSFFRLRRKRLEAEAAEAVAGFDVQGVRSLKQKAALLSGGNAQKLVIARE 425

Query: 433 LMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMH 492
              +P ++++  P+RG+DV A A ++  +      G AV++IS +L EVL ++DR+ VM 
Sbjct: 426 FSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAGAAVLVISEDLDEVLALADRIGVMS 485

Query: 493 EGDLMGTLDR 502
            G ++   DR
Sbjct: 486 GGRIVAEFDR 495



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 66/253 (26%), Positives = 120/253 (47%), Gaps = 18/253 (7%)

Query: 280 LMSVRDLRLDGVFKG---------VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDG 330
           + ++  ++L GV K            F    GE+  + G  G+G++++     G+   + 
Sbjct: 1   MSNLNAIQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPES 60

Query: 331 GEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQ 390
           G + ++   VR+S P  A      ++ +  KL   F   +V EN+++A LP   GN    
Sbjct: 61  GSLLINDNAVRLSGPRDASRYHIGMVHQHFKLVKPF---TVAENIQLA-LPEGPGNHAFS 116

Query: 391 ---QKALRALCEDMCKKLRVKTPSLE--QCIDTLSGGNQQKALLARWLMTNPRILILDEP 445
              ++ L AL + +  K      S++  +  ++LS   QQ+  + + L+   RILILDEP
Sbjct: 117 GSHRQRLAALEQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEP 176

Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505
           T  +  G    +   +   A +G AVI+++ ++ +V   +DRV VM  G  + TLD    
Sbjct: 177 TAVLTDGEAERLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTV 236

Query: 506 TQERVMQLASGMS 518
           +   +++L  G S
Sbjct: 237 SVPELVRLTVGES 249


Lambda     K      H
   0.321    0.137    0.391 

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: 643
Number of extensions: 37
Number of successful extensions: 6
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: 521
Length of database: 525
Length adjustment: 35
Effective length of query: 486
Effective length of database: 490
Effective search space:   238140
Effective search space used:   238140
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: 52 (24.6 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