Alignments for a candidate for PS417_11890 in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Trichormus variabilis ATCC 29413

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  423 bits (1088), Expect = e-123
 Identities = 229/502 (45%), Positives = 324/502 (64%), Gaps = 5/502 (0%)

Query: 21  PVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80
           P     +LE+  ++K F GV AL  V L + PG V ALMGENGAGKSTLMKI+AG Y  D
Sbjct: 12  PATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIAD 71

Query: 81  AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHRE 140
            GE+R+ GK V    P  A QAGI +I+QELN+ P++++ ENI++G E   G   +D + 
Sbjct: 72  EGEIRINGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRG-QFLDRKA 130

Query: 141 MHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200
           M     Q+L  L  +  P + VG L+IAE+Q VEIA+A+  +S IL+MDEPT+A++D+E 
Sbjct: 131 MELEAQQVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRET 190

Query: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260
             LF +I  L+  G  IIYI+H+M E++++AD ++V RDG YIG    + +    L+ MM
Sbjct: 191 ERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMM 250

Query: 261 VGRELSQLFP-VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVA 319
           VGR +   +   R+   G +++ VR++      +  SF L AGEILG+AGL+G+GRT V+
Sbjct: 251 VGRSMQDFYEHQRQSNPGPVVLEVRNISDGRKVQPASFQLRAGEILGLAGLVGAGRTEVS 310

Query: 320 EAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 379
             IFG      GE+ L+G+ + I  P  AI  G   + EDRK  GLF  +S  +N+ +  
Sbjct: 311 RLIFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKNIGLNR 370

Query: 380 LPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 439
           L   A  G +   ++  +  D  +   ++  +LE     LSGGNQQK LLARWL  NPR+
Sbjct: 371 LKQDANLGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLARWLAINPRV 430

Query: 440 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 499
           L+LDEPTRG+D+GAK+EIYR+IS L+++G+A++M+SSELPE++G+SDRV+VM EG L+G 
Sbjct: 431 LMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREGQLVGE 490

Query: 500 LDRS---EATQERVMQLASGMS 518
           LD S   E TQE +M  A+G S
Sbjct: 491 LDNSIGKEITQENIMHYATGAS 512



 Score =  113 bits (283), Expect = 1e-29
 Identities = 68/236 (28%), Positives = 130/236 (55%), Gaps = 8/236 (3%)

Query: 287 RLDGV--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISD 344
           R  GV   +GV+  ++ GE+  + G  G+G++ + + + G   +D GEI ++G+ V+I+D
Sbjct: 27  RFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRINGKGVKITD 86

Query: 345 PHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKK 404
           P  A + G  L+ ++  ++   P L+V EN+ M          F+ +KA+    + +   
Sbjct: 87  PGTARQAGINLIYQELNVA---PNLTVTENIFMG--SELTRGQFLDRKAMELEAQQVLAS 141

Query: 405 LRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYL 464
           L       +  + TL+   QQ+  +AR L  N RIL++DEPT  +       ++ +I  L
Sbjct: 142 LGASFAPTD-IVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEVIRKL 200

Query: 465 ASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSVR 520
            ++G+A+I IS  + E+  ++DR+ V+ +G  +G+L R E + +R++Q+  G S++
Sbjct: 201 RNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMVGRSMQ 256


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: 647
Number of extensions: 29
Number of successful extensions: 7
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: 517
Length adjustment: 35
Effective length of query: 486
Effective length of database: 482
Effective search space:   234252
Effective search space used:   234252
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.

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Steps (tab-delimited)
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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