Alignments for a candidate for BPHYT_RS16930 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Pseudomonas putida KT2440

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  338 bits (867), Expect = 3e-97
 Identities = 196/494 (39%), Positives = 286/494 (57%), Gaps = 12/494 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L    I K F   RALDG S  V  G VHGL+GENGAGKSTL+K+L G ++PD+G +++D
Sbjct: 6   LELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLLD 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G      S       GI  IHQE       TV E L  G        +++R  +R     
Sbjct: 66  GQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAARL 125

Query: 125 LEA-MGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
           L+   G+ L  NA + +LS A++QMV+I +ALL   RV+  DEP+ +L  RE E L ++V
Sbjct: 126 LDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRIV 185

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIAS----HPTLEGVTRDTIVSEMVG 239
           + LR D  A++YISH + EI  LCD  T+ R+GR +A     + +LE +TR      MV 
Sbjct: 186 QRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITR-----LMVN 240

Query: 240 REISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299
           RE+ ++Y   A P G +    +G+      Q    +VRRGEIVG  GLVG+G  EL+  +
Sbjct: 241 REVGELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSL 300

Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359
           +G      GE+ LDG+P+ +RS  EA+  G+ L PE+R+ +G+    +V EN  ++    
Sbjct: 301 FGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSR 360

Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419
           ++R+G+ L   +E  T    I+ L+IK      K+R LSGGNQQK  L++W A     + 
Sbjct: 361 FVRLGL-LSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCS-SLY 418

Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479
           +LDEP+ GIDVGAK EIY +I +L + G  ++++SS+LPE++G+ DRI VM +G I+   
Sbjct: 419 LLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARF 478

Query: 480 TRKDATEQSVLSLA 493
              +A    +L++A
Sbjct: 479 AAGEANSDRLLAVA 492



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 67/242 (27%), Positives = 109/242 (45%), Gaps = 9/242 (3%)

Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311
           P+ E+R   K          AS  V  G + G  G  GAG+S L+ ++ G      G LL
Sbjct: 4   PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63

Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371
           LDG+P    S  +  R GI    ++R    + A  TV E +      H  R G  LDR+ 
Sbjct: 64  LDGQPHGHFSPRQVERLGIGFIHQERL---LPARFTVGEALFFG---HERRFGPLLDRRS 117

Query: 372 EAETADRFI-KLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDV 430
           +   A R +     ++ P+        S   Q   I+   L +P  +V++ DEP+  +  
Sbjct: 118 QQREAARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKP--RVLVFDEPSVALVQ 175

Query: 431 GAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVL 490
                +  ++ +L + G AIV IS  L E+  + DR+ V+R GR   E++ ++ + + + 
Sbjct: 176 REVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQIT 235

Query: 491 SL 492
            L
Sbjct: 236 RL 237


Lambda     K      H
   0.320    0.136    0.385 

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: 651
Number of extensions: 36
Number of successful extensions: 9
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: 512
Length of database: 512
Length adjustment: 35
Effective length of query: 477
Effective length of database: 477
Effective search space:   227529
Effective search space used:   227529
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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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 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