Alignments for a candidate for glpV in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Halomonas desiderata SP1

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate WP_086511676.1 BZY95_RS20120 carbohydrate ABC transporter substrate-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_796
         (577 letters)



>NCBI__GCF_002151265.1:WP_086511676.1
          Length = 579

 Score =  685 bits (1768), Expect = 0.0
 Identities = 327/579 (56%), Positives = 422/579 (72%), Gaps = 7/579 (1%)

Query: 2   KMQFKAIA--FAAAALAMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKK 59
           ++Q  AIA     A+ A+        A A++ +D+ FQ STL++++Q+ E+ WF  AA+ 
Sbjct: 5   RIQLTAIAGSLLLASAALHAQTDDARAIAERLVDTHFQNSTLSREEQIEELLWFAQAAEP 64

Query: 60  LQAKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGK 119
            +     +I+ V+E +TTH +E   LA AFEE+TGI+V H++I EGD+V+ +QT MQ+G+
Sbjct: 65  FRGM---QINTVAEGLTTHVWERDVLAPAFEELTGIRVTHNIIGEGDLVDNMQTQMQTGR 121

Query: 120 SIYDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLY 179
           +IYDG+I+DSD IGTH RYG  +NL+  M     ++T P +DL D+IG ++TTGPDG +Y
Sbjct: 122 NIYDGYINDSDAIGTHIRYGTTINLSQAMENEWADFTLPTLDLDDFIGIQYTTGPDGSIY 181

Query: 180 QLPDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDG 239
           QLP QQFANLYWFR D F R+D++++F+  YGYDLGVP NW+AYE+IAEFFT  V+ IDG
Sbjct: 182 QLPAQQFANLYWFRYDWFQREDLQEQFREIYGYDLGVPTNWTAYENIAEFFTEHVREIDG 241

Query: 240 KPIYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASV 299
             +YGHMDYG++DPSLGWRF D+WLSMAG    G P G P+D+WGIRV D++  PVGASV
Sbjct: 242 VRVYGHMDYGRRDPSLGWRFHDSWLSMAGMGSPGIPFGNPVDDWGIRV-DEESRPVGASV 300

Query: 300 ARGGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTAD 359
           +RGG TN+PA+V+A+ K VDW++ YAP EA GMTFGEAGPVPAQG IAQQIFWYTAFTAD
Sbjct: 301 SRGGGTNAPASVFAMQKAVDWLRDYAPPEAQGMTFGEAGPVPAQGNIAQQIFWYTAFTAD 360

Query: 360 MTKPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYA 419
           M  P + V + +G P WRMAP P GPYW++GM+ GYQDVGSWTFF     ++  AAWL+ 
Sbjct: 361 MIDPSVAVTDDEGNPLWRMAPSPVGPYWEEGMKVGYQDVGSWTFFDSTPEDRRTAAWLFG 420

Query: 420 QFVTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVP 479
           QF  AKT SL+K M GLTPIRESDI S  MT+MAP+LGGLVEFYRSP    W+PTGTNVP
Sbjct: 421 QFTVAKTVSLEKLMAGLTPIRESDIFSDQMTEMAPRLGGLVEFYRSPNESMWTPTGTNVP 480

Query: 480 DYPKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHC-APKLNAKSDP 538
           DYP++A LWW+N+A  ++GE +PQ  +D LA  MD +MARL RA +     P LN + DP
Sbjct: 481 DYPRMAPLWWQNLAPVISGEISPQEGLDNLAGAMDNIMARLARANVFEAYPPVLNEERDP 540

Query: 539 NKWLSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR 577
             WLS   AP  KL +E P+G TI Y  +++ W    TR
Sbjct: 541 EYWLSQPGAPKAKLDDEMPQGTTIPYDQMMEEWMAAGTR 579


Lambda     K      H
   0.315    0.132    0.412 

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: 1156
Number of extensions: 49
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 577
Length of database: 579
Length adjustment: 36
Effective length of query: 541
Effective length of database: 543
Effective search space:   293763
Effective search space used:   293763
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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