Alignments for a candidate for rbsA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas putida KT2440

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  344 bits (883), Expect = 4e-99
 Identities = 211/499 (42%), Positives = 298/499 (59%), Gaps = 17/499 (3%)

Query: 11  SPLLTLSGIGKRYAAP-VLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69
           +P+L L GI K + A   LDG  L +  G V  L GENGAGKSTL K++ G+    AG +
Sbjct: 3   TPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSL 62

Query: 70  MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFG-WIDRK-KLAE 127
           +LDGQP+   S  Q E LGI  + QE  L    ++ E LF     RRFG  +DR+ +  E
Sbjct: 63  LLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGH-ERRFGPLLDRRSQQRE 121

Query: 128 AARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVEL 187
           AAR   +  GL  L     +G+L    QQMV+I R L+   R L+ DEP+  L  REVE 
Sbjct: 122 AARLLDDYFGL-RLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVER 180

Query: 188 LFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMA- 246
           L   ++RLR +G+AI+YISH L+E++ + DR+ VLR+G+ V        S EQ+ +LM  
Sbjct: 181 LLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVN 240

Query: 247 ---GEL-TKVDLDAEHRRIGAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIGSGRTE 302
              GEL  KV + A     GA +L +RGLGRA       L +  GE++G+ GL+GSG  E
Sbjct: 241 REVGELYPKVAVPA-----GALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKE 295

Query: 303 LLRLIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNT 362
           LLR +FG    + GE+ +    +P  +RSP++AV  G+A++ E+R+ QG+ L  ++  NT
Sbjct: 296 LLRSLFGLAPPDSGEVRLDG--QPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENT 353

Query: 363 SLANLGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYR 422
           +LA L    R G+L  A E     + +++LRI++        +LSGGNQQKV +A+W  R
Sbjct: 354 TLAALSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFAR 413

Query: 423 DCPIMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGR 482
              + L DEP+ GID+GAK +IYRL  EL  +G G+L++SSDL EL+ +CDRI VM  G 
Sbjct: 414 CSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGA 473

Query: 483 IADTFSRDDWSQERILAAA 501
           IA  F+  + + +R+LA A
Sbjct: 474 IAARFAAGEANSDRLLAVA 492



 Score = 87.8 bits (216), Expect = 9e-22
 Identities = 68/252 (26%), Positives = 117/252 (46%), Gaps = 8/252 (3%)

Query: 1   MQPNDSLSQGSPLLTLSGIGKRYAAPVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICG 60
           + P  ++  G+ LL + G+G+   A    GIDL +R G+++ LTG  G+G   L + + G
Sbjct: 246 LYPKVAVPAGALLLDVRGLGR---ARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFG 302

Query: 61  LVDASAGGMMLDGQPYAPASRTQAEGLGIRMVMQELN---LIPTLSIAENLFLEKLPR-- 115
           L    +G + LDGQP +  S  +A   G+ ++ +E     +   LS+ EN  L  L R  
Sbjct: 303 LAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFV 362

Query: 116 RFGWIDRKKLAEAARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDE 175
           R G +   +        +E + +        V  L  G+QQ V +A+         +LDE
Sbjct: 363 RLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDE 422

Query: 176 PTAMLTNREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGR 235
           P+  +       ++  I  L  EG  ++ +S  L EL  + DRI V+  G +      G 
Sbjct: 423 PSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGE 482

Query: 236 YSTEQLVQLMAG 247
            ++++L+ +  G
Sbjct: 483 ANSDRLLAVATG 494



 Score = 85.1 bits (209), Expect = 6e-21
 Identities = 71/255 (27%), Positives = 120/255 (47%), Gaps = 19/255 (7%)

Query: 261 IGAPVLRIRGL----GRAPVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQG 316
           +  PVL +RG+    G    +  ASL + AG V G+ G  G+G++ L++++ G  R + G
Sbjct: 1   MSTPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAG 60

Query: 317 EIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGML 376
            + +    +P    SP+   + GI  + ++R     LLP   +V  +L        G +L
Sbjct: 61  SLLLDG--QPHGHFSPRQVERLGIGFIHQER-----LLPARFTVGEALFFGHERRFGPLL 113

Query: 377 DHAAESSVA----QDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEP 432
           D  ++   A     DY   LR+ + ++    GELS   QQ V I R L     +++FDEP
Sbjct: 114 DRRSQQREAARLLDDYFG-LRLPANALI---GELSSAEQQMVQIVRALLIKPRVLVFDEP 169

Query: 433 TRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTFSRDDW 492
           +  +       + R+   L   G  ++ +S  L+E+  +CDR+ V+  GR     S  + 
Sbjct: 170 SVALVQREVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNT 229

Query: 493 SQERILAAAFSGYVG 507
           S E+I     +  VG
Sbjct: 230 SLEQITRLMVNREVG 244


Lambda     K      H
   0.320    0.137    0.390 

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: 697
Number of extensions: 40
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 522
Length of database: 512
Length adjustment: 35
Effective length of query: 487
Effective length of database: 477
Effective search space:   232299
Effective search space used:   232299
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