Alignments for a candidate for araVsh in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Sinorhizobium meliloti 1021

Align ABC transporter related (characterized, see rationale)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Smeli:SMc02325
          Length = 503

 Score =  349 bits (896), Expect = e-100
 Identities = 190/498 (38%), Positives = 309/498 (62%), Gaps = 7/498 (1%)

Query: 1   MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60
           M   + L+ ISK +PGV+AL DVSL L+ G V AL+GENGAGKSTLVK++TG    D G 
Sbjct: 1   MKPAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGT 60

Query: 61  ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGLIHFKKMYA 119
           I        F T + A +AG++ ++QE  L   L+VA+N+FLG+ PR R GLI +K++ A
Sbjct: 61  IRLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNA 120

Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179
           DA+A+L +   D D +  L D  IA + L+AIAR +++ A+V+++DEPTA+L  KE+  L
Sbjct: 121 DAQALLGRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHEL 180

Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239
           + ++ +LKA G A++FI+H  D++++I+DR TV R+G  IGE L A++ Q  L+  M+GR
Sbjct: 181 YDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGR 240

Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299
           ++      K+     VT  + VL ++         + +N  + +G+ +G  GL+G+GRSE
Sbjct: 241 AVGSVYPKKE-----VTIGQPVL-TVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSE 294

Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359
              ++ G+    +G++ L G+ L +  P +AI AGI   PE+R   G I  + I +N+ L
Sbjct: 295 FMQSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTL 354

Query: 360 ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419
              +      +L    +  +A+ +  +L +     D+ +  LSGGNQQKV++A+WLA  P
Sbjct: 355 PSLSHTSRSGFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRP 414

Query: 420 ILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAV 479
            +++LDEPT+GIDIG+ A +   +  L  +G+S+++ SSE+ E++  S++V+V+R+    
Sbjct: 415 KVIILDEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVA 474

Query: 480 RELSGAELTSQHVMQAIA 497
                +ELT++ +++A A
Sbjct: 475 GRYERSELTAEKLVRAAA 492



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 63/232 (27%), Positives = 113/232 (48%), Gaps = 14/232 (6%)

Query: 21  EDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAG 80
           ED++  L  GE+    G  GAG+S  ++ + G      G +   GE     +P +A +AG
Sbjct: 270 EDINFELRRGEILGFYGLVGAGRSEFMQSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAG 329

Query: 81  ISTVYQE---VNLVPNLTVAQNLFLGY--EPRRLGLIHFKKMYADARAVLTQFKLDIDVS 135
           I  V +E      +  + + QN+ L       R G +   + +A AR    ++   +D+ 
Sbjct: 330 IVYVPEERGRQGAIIGMPIFQNVTLPSLSHTSRSGFLRLAEEFALAR----EYTSRLDLR 385

Query: 136 APLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190
           A   D  +       QQ + IA+ +A   KV++LDEPT  +D      +   +++L A+G
Sbjct: 386 AAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILDEPTKGIDIGSKAAVHAFMSELAAQG 445

Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           ++++ ++  + ++  +SDR+ V+R G+  G Y  +EL   KL+ A  G   Q
Sbjct: 446 LSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERSELTAEKLVRAAAGIETQ 497


Lambda     K      H
   0.319    0.136    0.377 

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: 583
Number of extensions: 25
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: 499
Length of database: 503
Length adjustment: 34
Effective length of query: 465
Effective length of database: 469
Effective search space:   218085
Effective search space used:   218085
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 17 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:

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 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