Alignments for a candidate for PS417_11890 in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Lactobacillus shenzhenensis LY-73

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000469325.1:WP_022528026.1
          Length = 515

 Score =  378 bits (970), Expect = e-109
 Identities = 199/498 (39%), Positives = 312/498 (62%), Gaps = 4/498 (0%)

Query: 21  PVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80
           PVD   +L I  +SK F     L  + + V+ GSV+ LMGENGAGKST+MK + GI   D
Sbjct: 16  PVDSDVMLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRD 75

Query: 81  AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHRE 140
            G+  L GK V+F  P  AL+ GIAM+HQELN     S+ +N+++GR  +N   ++D R+
Sbjct: 76  EGKFYLDGKEVSFQGPKDALENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQ 135

Query: 141 MHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200
           M R   +L  RL + ++  + +  +S+++RQMVEIAKA+SY S ++++DEPTS++  +EV
Sbjct: 136 MRREATELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEV 195

Query: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260
             LF ++  LK QG  II+I+HKM+EVF I DEV+V RDG  +  ++    + + L+  M
Sbjct: 196 DKLFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAM 255

Query: 261 VGRELSQLFPVREKPIGDLLMSVRDL--RLDGVFKGVSFDLHAGEILGIAGLMGSGRTNV 318
           VGR L   FP  +  +G  ++ V  L  +     + ++F +  GEI G+ GL+G+GRT +
Sbjct: 256 VGRPLDNRFPPVDNVVGKTILQVSHLSTKFSPYLQDITFSVGQGEIFGLYGLVGAGRTEL 315

Query: 319 AEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 378
            E IFG+     G +  +G+    +    A++ GFA++TE+RK +GLF   S+  N  + 
Sbjct: 316 LETIFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTIT 375

Query: 379 VLPHY-AGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 437
            L  Y  G    +QK  +A  +++ + +  KT   ++ I +LSGGNQQK ++ +WL   P
Sbjct: 376 NLDAYKRGVALSEQKMTKATLKEI-QVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLP 434

Query: 438 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 497
           ++ ++DEPTRGIDVGAK EIY LI  +A +G  +I++SSE+PE+LG+++R+ VM  G L 
Sbjct: 435 QLFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVMSNGRLA 494

Query: 498 GTLDRSEATQERVMQLAS 515
           G ++  +  QE +++L++
Sbjct: 495 GIVNTKQTNQEELLRLSA 512



 Score = 95.5 bits (236), Expect = 4e-24
 Identities = 60/250 (24%), Positives = 132/250 (52%), Gaps = 10/250 (4%)

Query: 272 REKPI-GDLLMSVRDLRL----DGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326
           +E P+  D+++S+R L      + V   +  D+  G ++G+ G  G+G++ + + +FGI 
Sbjct: 13  QEPPVDSDVMLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIK 72

Query: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGN 386
             D G+  LDG+ V    P  A+E G A++ ++   +      SV++N+ +   P  A  
Sbjct: 73  TRDEGKFYLDGKEVSFQGPKDALENGIAMVHQELNQA---LDRSVVDNLFLGRYPVNA-L 128

Query: 387 GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPT 446
           G + ++ +R    ++ ++L + T +L Q +  +S   +Q   +A+ +  + ++++LDEPT
Sbjct: 129 GVVDERQMRREATELFRRLGM-TVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPT 187

Query: 447 RGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEAT 506
             +      +++ ++  L  +G+++I IS ++ EV  + D V V+ +G L+ T   ++  
Sbjct: 188 SSLMAQEVDKLFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTN 247

Query: 507 QERVMQLASG 516
              +++   G
Sbjct: 248 MNELVKAMVG 257


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: 586
Number of extensions: 24
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: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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:

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